The USS Yamato waits to begin a new 5-year mission at Deep Space One, at the edge of Federation space on the border between the Alpha and Beta Quadrants. A group of new crewmembers, most of them recent graduates from Starfleet Academy, are catching a ride on a long-range shuttlecraft being transferred to the ship when the shuttle encounters some trouble. When the shuttle drops out of warp to make a course correction it strikes a gravitic mine left over from the Federation-Klingon War nearly 15 years earlier. The shuttle crash lands on a nearby Class L planet where they must survive long enough to repair the shuttle as the likelihood of rescue is low. They fend off attacks by predatory canids native to the world, and by a group of Klingons who had crashed here during the war and had reverted to animalistic savagery and cannibalism in the years since. The discovery of the Klingons proves beneficial in the end, as the crew are able to locate the wreck of the Klingons' ship and scavenge enough parts to let the shuttle reach space. Once out of the planet's atmosphere they are able to send a distress signal and are rescued by the USS Yamato herself.
At Deep Space One, new crewmembers assigned to the USS Yamato undergo orientation activities prior to the ship's departure on its new 5-year mission. The new crew are organized into cross-disciplinary teams to encourage exposure to diverse experiences. One of these teams is Delta Shift Team Five, known as Delta 5 for short, and the core of this team are the junior officers who had been involved in the shuttle crash. This was not a coincidence but rather a choice by the XO, Commander Cartwright, who felt that the group's prior experience together would be a benefit. Several other junior officers are also assigned to Delta 5 and it is not long before they have their first mission. While surveying the Mutara Nebula the USS Yamato discovers a Class M world and survey teams made up of officers from Delta shift, including one consisting of members of Delta 5, are beamed down. When Delta 6 disappears and Delta 5 comes under attack by the very terrain of the planet it is discovered that the planet is a single macro-organism. The flora and fauna, and the very ground itself, react like an immune system response against the invading organisms the survey teams represent. Delta 5 and the remaining survey teams are able to escape the planet with help of the Yamato, before there any additional casualties.
The USS Yamato encounters a spatial anomaly that schisms the ship's interior. Sections inside the ship become cut off from the rest of the vessel, instead now looping back in on itself. The changes to the interior layout are not remaining constant either, and when crewmembers are caught in an area that is shifting it proves dangerous, even fatal in some cases. Trapped in the area of the ship around their crew quarters, Team Delta 5 and the other crew confined with them work to understand what has happened and establish communication with other parts of the ship. When contact is established with the Bridge, Delta 5 help coordinate efforts with Main Engineering and Deflector Control and the Yamato is successfully freed from the anomaly.
The USS Yamato answers a distress call and finds a Federation transport under attack by a Klingon battle cruiser. As the Yamato chases off the Klingon vessel, Team Delta 5 is sent to the transport to assist with repairs and casualties, but finds the transport's crew to be standoffish and uncooperative. The two groups were forced to work together when a Klingon scout vessel arrived and attacked. During the battle some members of Delta 5 learn the truth: the crew of the transport are actually Klingons, descendants of those who suffered from the Augment Virus that caused them to appear human. These Klingons had been intelligence operatives, sent undercover into the Federation during the early years of the Organian Peace Treaty. After a recent change in the Klingon High Council, these activities have been curtailed and the human-looking Klingons (the QuchHa' in the Klingon language) now found themselves persecuted and stripped of honor. Faced with a choice between cosmetic surgery or exile to prison planets, this group elected to flee the Empire to find a new home. They still consider themselves loyal Klingons and do not trust the Federation, so they will not request asylum, but the Empire will not let them go and so they have become hunted. Ens. Dawnslight is able to get the transport's warp engines back online and they are able to escape from the Klingon scout long enough to reach the USS Yamato. As the transport crew refuses to request asylum, Capt. Sloane opts to let the transport and her crew go, but informs Starfleet Command. Two weeks later the transport is reported to have been destroyed, but the fate of her crew is unknown.
Team Delta 5 are conducting a ground survey on planet VC298-IV, an uninhabited Class M world, when they detect an intense energy burst at the outer range of their tricorders. Soon after the team realizes that they are no longer able to make contact with the Yamato. After nightfall the team attempts to visually identify the Yamato based on its known orbit, but there is no sign, implying the ship is no longer in orbit around the planet. The team decides to head towards the where they had detected the energy burst. It takes a few days of overland travel, during which there is still no sign of the Yamato, before the team comes to an ancient ruin. They find a way into a buried complex where ancient carvings tell the tale of a race of humanoids who had once been enslaved by inhuman entities and who had overthrown their oppressors. This world had been one of many, but the humanoids drove off their former masters and took control of their great city on this world. Delta 5 explores further and discovers there is indeed a massive city beneath the ground here, in the middle of which they find an ancient control center. The center contains advanced technology controlling a still-operating millennia-old planetary defense system. It becomes apparent that the Yamato must have fallen victim to this defense system, though what happened was not clear The team tries to figure out the technology, but have made little progress when the defense system begins to activate again. On a monitor they can see that the Yamato is approaching the planet again, having apparently recovered from whatever had occurred previously. With no time to figure out the machine, the team reluctantly uses their phasers to destroy the defense system controls so it does not attack the Yamato again. The team are beamed back aboard where they report their discoveries.
Under the terms of the Organian Peace Treaty between the Federation and the Klingon Empire, planets that fall in the treaty zone have a choice which of the two governments they can choose to ally with. With the treaty enforced by the powerful Organians, diplomacy and espionage become the tools for convincing these worlds which of the two is their best option. The Lorealyn system is one such case, and the Federation has sent one of their best ambassadors to help ensure that the system sides with them rather than the Klingons. Delta 5 are assigned to escort the ambassador, crewing the Mission class courier USS temple. En route the courier ship is intercepted by a Klingon battle cruiser and Delta 5 and the ambassador are captured to prevent the Federation from succeeding in the negotiations. Delta 5 are able to escape from their cells and attempt to locate the ambassador, who was not held with them. With surprise on their side, and an initial reluctance by the Klingons to kill them in case it attracted the attention of the Organians, the team reaches the shuttle bay where the Temple is being kept. Gaining access to the Temple, they use the ship's sensors to locate the ambassador and beam him aboard the courier ship. They blast their way free to discover they never left the Lorealyn system, and the revelation of the Klingons' actions tilts the negotiations in favor of the Federation.
A Starfleet Monitoring Station detects the fragment of a distress signal and the USS Yamato is sent to investigate. The Yamato discovers the Soyuz Class USS Europa adrift with minimal power readings and no life signs aboard. Cmdr. Cartwright leads a boarding team to investigate and they find no trace of the crew and the vessel running on auxiliary power only. Further examination reveals that the warp core has been ejected and the computers cores have been wiped clean by some kind of radiation pulse. After the initial investigation follow-up teams consisting of Delta 3 and Delta 5 are sent over for more detailed analysis. The more they investigate, the more the mystery deepens. There is evidence of phaser fire in various parts of the ship, and the signs point to the crew battling each other. In engineering teams discover that the impulse reactors had been overloaded to produce a dangerous radiation pulse. This pulse is what is responsible for the erasure of the computer cores and would have been lethal to anyone in the aft section of the ship. A phaser is recovered near one of the main transporter rooms, and it is discovered to be set to maximum power. The transporter systems also appear to have been left active, though with the computers erased there is no information on how it might have last been used. The investigative teams continue to conduct scans and look for clues until they are finally recalled to the Yamato to review what has been learned. Captain Sloane plans to send more teams over, but before she can a message from Starfleet orders the Yamato to return to its original mission and that a dedicated science vessel will arrive shortly to take over the investigation of the Europa.
Even though Captain Sloane offered for the Yamato to take the lead in investigating what happened to the Europa, Starfleet has sent a science vessel to take over. Despite this, the Captain has kept the crew working on analyzing the data they had collected from the Europa. Along with this, Captain Sloane has also ordered the Yamato to follow a course that roughly follows the direction the Europa was believed to have been traveling before it dropped out of warp. The crew slowly piece together evidence of what appeared to be a mutiny or other conflict among the crew, where one group was trying to kill the rest, possibly in a desperate attempt to stop the ship from getting somewhere. Phasers had been set to disintegrate, transporters were used to beam people into nothingness, and finally the warp core was ejected and the impulse reactors overloaded to produce a radiation pulse that destroyed living tissue and wiped the computer cores of data. After a couple of days of this a medical emergency is declared when it is discovered that the landing parties had brought some kind of pathogen over from the Yamato. Despite efforts at quarantine the infection spreads throughout the ship. The unknown pathogen transforms its victim's tissues into some form of living stone, and infection rate accelerates as the crew try and fight it. Before they can rendezvous with a science ship the entire crew of the Yamato have been fully transformed, at which point an alien entity takes mental control of them and commandeers the ship for an unknown purpose.
The captured Yamato is brought to an unknown world beyond the borders of the Federation in the Beta Quadrant. In orbit around this world are six other vessels including a Klingon D-7, a Romulan Bird of Prey, and a Gorn and an Orion ship in addition to two unrecognized vessels. Like the Yamato, the crews of these vessels have also been transformed and dominated. The ship crews have been turned into pawns of seven alien beings who are vying for control of their people. Rather than go to war on their own these beings take crews of starships and transform them into soldiers and set them against each other on a selected planet in a proxy war so that their own worlds will not be harmed in this war of succession. The transformed crews can still think independently, but they have no control over their transformed bodies. Though the alien's control over their bodies seems absolute, Lt. JG Sevek finds that his training in the Vulcan Kohlinahr discipline gives him the mental strength to take temporary control of his own transformed body. Sevek takes advantage of his momentary freedom to locate Lt. S'Chal and using a Mind Meld helps the Aenar also free himself. Sevek's Vulcan mental discipline combined with S'Chal's native ability to disrupt telepathic signals lets the pair act freely and they seek out several of their teammates in Delta 5 as well as Captain Sloane. This small group are then able to beam back up to the Yamato. Based on the earlier investigations they realize that individuals with high psi potential seem to have the best ability to resist the control. Based on this Captain Sloane points to the Romulans as potential allies, since their shared physiology with Vulcans may give them an edge. The group locate and beam up the commander of the Romulan vessel, Commander Sheva, and help her break the mental control of the alien controlling her and her crew. Sheva reveals what the Romulans had discovered while they were similarly trying to stop the infection transforming their crew, and with this information the two captains and the members of Delta 5 are able to disrupt the effect that had transformed the crews. Captain Sloane volunteers as a test subject and the procedure works. Together they figure out a way to broadcast this disruption effect across the planet, which frees all the captive crews. Without their proxy soldiers the aliens flee back to their own worlds and the captive crews all return to their own ships. Though most of the vessels are hostile to each other, additional Federation vessels are detected approaching the planet, thanks to the Yamato having gotten a message out before the crew had been completely transformed. This is enough to dissuade any of the other vessels from starting hostilities and so they all go their separate ways.
A little more than a year after starting her Five Year Mission the USS Yamato is back where she started, at Deep Space One where Starfleet has ordered her so that both the vessel and her crew can be examined for any lingering effects of their recent transformation at the hand of an unknown alien being. The USS Europa is also there undergoing examination, with the science vessel USS Sigma leading the investigation. Also present is the USS Bell, a vessel assigned to Division 14, a specialized group within Starfleet tasked with handling extraordinary science and medical related phenomena afflicting Starfleet personnel. The entire crew of the Yamato are being subject to examination by the Division 14 experts, while the Science teams from the USS Sigma examine the Yamato herself. Once their interviews and examinations are done, several members of Delta 5 take advantage of the base entertainment facilities before the Yamato departs again. Sevek is promoted to full Lieutenant and S'Chal starts working with a Vulcan doctor from Division 14 to develop his inherent telepathic abilities.
The Yamato conducts an unusual First Contact with a pre-Industrial society, the Atyansa, who somehow has full awareness of the existence of space travel and alien intelligences, including the Federation, and who specifically requested the Yamato for the First Contact. The initial contact team from the Yamato is further surprised when the natives indicate they were expecting the members of Delta 5 to be the contact team. Delta 5 beam down to the planet and are shown ancient texts that appear to describe the team and contain a legend of them undertaking a quest to avert disaster to this world. While Delta 5 are on the planet a Klingon cruiser arrives in orbit. While the Yamato delays the Klingons, Delta 5 decides to try and complete the quest. Led by the son of the village chief they evade strange illusory creatures and a Klingon landing party to discover an advanced computer housed in a mountain cavern. The computer was constructed by the ancestors of the Atyansa and had used its advanced predictive capabilities to bring lure the Yamato and Delta 5 here to get the Federation's assistance preventing the Klingons from taking over and acquiring its capabilities. The Klingons are sent away with the computer's help and the Federation takes the planet as a protectorate.
The Yamato is sent to explore a recently discovered phenomenon called a dark nebula, designated Styx by Federation astronomers. Starfleet probes have been lost inside the dark cloud, so the Yamato must go in blind. Inside the outer shell the ship discovers that the nebula conceals a most unusual system. At the heart of the nebula is a spinning neutron star, a pulsar but most unusually an irregular one. Even stranger, the pulsar has a planet circling it in a highly eccentric orbit. While Yamato continues to examine the pulsar and the rest of the nebula Delta 5 are beamed down in environment suits to examine the orbiting world. The planet is dead, with barely a trace of atmosphere but scattered around the surface are the remains of giant stone cities. The cyclopean structures are reminiscent of the architecture of the buried city on VC298-IV so Delta 5 makes a careful record. Heading back to their beam down point, the team discover that the transporter pattern enhancers they had left at the site are missing and there are nearby life signs. The team are attacked by Orion pirates, but manage to fight them off. Recovering the pattern enhancers they beam back and discover that the Yamato has been boarded by Orions after the ship was ambushed by a pirate vessel and the enemy has nearly taken control of the secondary hull. Since they had environment suits, Delta 5 are able to do an EVA to circle around to shuttle bay and launch an attack against the Orions from the rear. The two-front assault ends the boarding action, and using the pirates' own boarding shuttle they take the fight to the Orion vessel. The vessel is disabled and towed out of the nebula to await Federation authorities to take the pirates into custody.
While cataloguing astronomical phenomena in a remote sector of the Beta Quadrant the Yamato detects a radio signal of intelligent origin. The radio signal turns out to be a sublight automated distress signal of old, but discernibly Federation origin. Checking old records, coding in the signal identifies it as belonging to the Bonaventure class USS Vanguard (NCC-1003), one of the earliest Federation classes of starships and in this case a vessel that disappeared more than a century earlier in 2168. The signal is tracked to a star system far out from the edge of Federation space. The red dwarf system, in Starfleet records simply as Sigma Taurii, has three worlds; an inner Class M world, a small Class J gas giant, and a large Class I gas supergiant. There is no sign of anything on the Class M world, but it is found that a subspace beacon from the Vanguard had been left on an outer moon of the gas supergiant. The beacon itself had been discovered there by a previously unknown intelligent aquatic species from the subsurface ocean of one of the inner ice moons. The Yamato initiates First Contact with the aquatic species and helps them save their moon from a cometary collision. In exchange the species, the Gith, give the Yamato access to the recovered beacon. The beacon itself contains little information about the fate of the Vanguard, other than it most likely left the system after leaving the beacon.
The Yamato is in orbit around the planet Ansalom Prime for resupply and has allowed the crew to take shore leave to enjoy many of the attractions on the neutral world. Sevek, Armitage and Vasquez of Delta 5 choose to visit a sideshow at the Silver Circus, an exotic traveling show that had recently set up shop on Ansalom. The Host at the sideshow is weaving a tale when he seems to single out the three members of Delta 5 in attendance, and they suddenly find themselves plunged into darkness. Emerging from the darkness the trio find themselves in an outdoor amphitheater under a uniform grey sky. At the same time, the trio's disappearance has come to the attention of their teammates on the Yamato and the ship starts to try and locate them. Back in the amphitheater the three are put on trial by energy beings called the Aerolith, accused of being Servants of Darkness. Wondering what this means, Armitage eventually surmises it may have been the team's encounters with the strange ancient ruins on VC298-IV and on the dead world in the Styx dark nebula. The Aerolith accept this may be the case and tell of a time eons in the past when the early races of the galaxy banded together to banish a great evil force and erect a barrier to keep it out. By this point the Yamato have discerned that the three have been taken out of phase and are able to locate them on sensors. They beam the three out just as the Aerolith give a warning that the barrier is weakening. Afterward there is no sign of the Host and no clue as to where the Aerolith have gone, so the Yamato can only log the warning and guess what this threat might be.
The Yamato was playing host to some religious pilgrims from a group called the Wanderers when they receive a distress call from a freighter under attack by Klingons. The arrival of the Yamato causes the Klingons to withdraw and so the Starfleet vessel takes the damaged freighter in tow. The freighter's captain is a bearded man named Kristopher Kerstman and his ship is crewed by diminutive Roylans. Kerstman and his crew are brought aboard the Yamato since the freighter's life support was damaged, and Delta 5 are assigned to keep an eye on the new guests. This becomes necessary as the Roylans are curious tinkerers who keep removing panels and climbing into Jefferies tubes, and Kerstman himself keeps insisting on handing out small robotic toys he claims to have designed himself. The Yamato tows the freighter to Alpha Polaris, where Kerstman says his factory is, but when they arrive there the Klingons return and attack the site on the surface. The factory site erupts in a massive explosion, much larger than expected and it engulfs the Klingon cruiser and destroys it. Scans show there were large amounts of dilithium at the site, and this directs suspicion towards Kerstman. When the robotic toys are examined they are discovered to conceal complex spy gear, revealing Kerstman's plot to give the toys to senior military and political figures in order to gather and sell secrets from the Federation, Klingons, Romulans and other powers. Further investigation reveals the Kerstman is in reality the galactic con man Harcourt Fenton Mudd and he is taken into custody. Innocent in Mudd's scheme, the Roylans are given a new home by the Wanderers when Delta 5 suggests that the Wanderers could use the Roylans' engineering talents to help keep their ships operating.
A stellar survey is interrupted by the arrival of a long-range shuttle with a mysterious passenger. The Yamato is diverted to a new destination, and upon arrival the senior members of Delta 5 are called to a briefing. In the briefing they learn the identity of the ship's mysterious guest, it is Commander Spock, the famed Vulcan science officer from Captain Kirk's Enterprise. In the classified briefing it is explained that the present location, labeled on charts as a navigation hazard, is the sight of an unusual phenomenon - a spatial rift. It is explained that three years earlier the USS Hood had been lost while researching the rift and the USS Yamato, under its previous crew, had been responsible for rescuing the surviving members of the Hood's crew. Spock explains that he has devised a means to traverse the rift and proposed a plan to Starfleet to recover the Hood. Starfleet agreed and gave Spock permission to use the Yamato in his plan, and Spock has selected the members of Delta 5 to assist him. It is explained that the mission is highly classified and dangerous, and thus participation is voluntary, but Delta 5 are convinced to participate. They are given drugs to protect them against the dangerous physiological effects of the rift, and using the experimental equipment in Spock's shuttle they enter the rift and locate the Hood adrift within. Once they have boarded the Hood, the team with Spock transfer the equipment from the shuttle and work to install it in the Hood, which should enable them as a skeleton crew to pilot the Hood out of the rift. It is gruelling work, especially with the mental effects of the rift that begin to afflict some of them despite the medication. The installation is successful in the end and Spock enters the navigational data. When the Hood emerges from the rift, however, Delta 5 do not see the Yamato but instead the Enterprise, the ISS Enterprise; they have traversed the rift into the Mirror Universe!
Delta 5 have been taken into the Mirror Universe by that dimension's Spock who had been posing as his main universe counterpart. Having salvaged the USS Hood to use in his effort against the despotic Terran Empire, Spock has a plan to acquire another vessel. Spock reveals he specifically chose Delta 5 to assist him because he felt they would be an asset for. In this universe, much like the main one, the members of Delta 5 had crash landed on a desolate planet; but in this universe they were killed. The ISS Yamato remained unaware of their deaths, however, and Spock wants Delta 5 to impersonate their dead counterparts and help him capture this universe's Yamato. In exchange for their assistance Spock promises to return them to the main universe. After some debate the six agree to assist Spock and they are given Terran Empire uniforms and briefed on the backgrounds of their deceased counterparts. Delta 5 take their counterparts' shuttlecraft and rendezvous with the ISS Yamato. The deception works and Delta 5 are able to infiltrate the Yamato, despite the disturbing nature of interacting with Mirror Universe counterparts to their commanders and fellow crew. They are able to disable the Yamato's defenses as Spock's allies arrive in the USS Hood, itself disguised as its Mirror Universe counterpart. With Yamato's shields disabled the Hood uses its phasers to stun the crew and seize the Terran vessel, adding a third ship to Spock's growing rebel fleet. True to his word Spock is able to return Delta 5 to the main universe where they return safely to the USS Yamato.
In the wake of Delta 5's encounter with the Mirror Universe the Yamato is ordered to the nearest Federation world. Starfleet keeps knowledge of the Mirror Universe a closely guarded secret so have dispatched a specialist team to debrief Delta 5 and the Yamato's senior officers. The team is made up of three officers from Starfleet Intelligence, a Division 14 medical specialist, and one man from an unidentified division. Once the medical specialist verifies that Delta 5 were not replaced by their Mirror Universe counterparts, the intelligence officers and the mystery man subject each member of the team to intense questioning. From his past experience, Lt. Drake surmises that the mystery man is a representative of the highly secretive Section 31, which tells him that they are worried of potential threats from the Mirror Universe. The line of questioning seems to support this theory, as the intelligence officers assess the potential of an invasion from the Mirror Universe. It takes many hours of questioning and re-questioning, but in the end the investigators seem to be satisfied that there is no imminent threat of invasion. In the end Delta 5 are released and Yamato is permitted to grant shore leave on Pacifica.
Since encountering the pilgrims called the Wanderers and learning of the Omen, the stellar phenomenon they follow across space, the astrophysics department on the USS Yamato has been working on a side project to track and identify the phenomenon. Reports of the Omen varied, but were generally consistent around it being a luminous object like a comet or a star appearing in the sky for a brief period. In cases where the observers got a good look it was often described as being a rainbow or kaleidoscope of colors. The effort pays off when the science team realizes the object has been hard to track because it is moving at close to the speed of light. The Yamato is able to locate the object and adjusting for the distortion from its speed they are able to discern it is a space vessel of some kind. Matching speed with the Omen the Yamato identifies it as the long-lost USS Vanguard, a century-old vessel that the Yamato had recently discovered an emergency beacon from. Emergency teams beam aboard and are able to slow the vessel's speed and discover what happened to her and her crew. According to the logs the Vanguard had encountered an anomaly that somehow brought them across thousands of light years, far beyond what had been the boundaries of known space a century ago. Having taken heavy casualties and with their warp drive damaged the Vanguard resupplied at the star system the Yamato had recently found their beacon at and then attempted to return to Federation space. When the warp drive failed completely they decided to travel at sublight speeds, rigging their impulse engines to accelerate them to close to the speed of light where relativistic effects would slow the passage of time for them so that they might survive long enough to reach Federation space. The plan worked for a time, but an error in navigation led to the ship being struck by the beam from an unidentified pulsar, a beam that their relativistic velocity caused to be shifted into higher levels of energy, enough to punch through the Vanguard's shields and give the crew a lethal dose of radiation. The last survivor was the Chief Engineer, who had been partially shielded from the radiation in engineering but had still taken an ultimately lethal dose. After cremating the remains of his crewmates the engineer set the ship systems on automatic and arranged for his own body to go into stasis in Sick Bay after his imminent death. Thanks to his efforts the life support systems had successfully cleansed the ship of radiation, enabling the eventual recovery of the ship by someone, in this case the USS Yamato.
Based on data recovered from the long-lost USS Vanguard, Starfleet dispatched a science ship to the position where the Vanguard encountered the anomaly that stranded it thousands of light years from home. The science ship went missing and Starfleet sent the USS Yamato to see if it had emerged in unexplored space much as the Vanguard did before it. To help narrow down the point where the Vanguard had emerged a century earlier the Yamato enlists the aid of the Gith, the aquatic inhabitants of an ice moon who had discovered the Vanguard's beacon. A team of Gith come aboard the Yamato and, with their uncanny abilities in higher dimensional mathematics, are able to help locate the emergence point. Investigating the area, the Yamato discovers the wreckage of the missing science vessel, the USS Korolev, which appears to have been destroyed by a warp core breach. While examining the wreckage the Yamato also detects a subspace anomaly, possibly the location where the Korolev emerged into this region of space. They also detect another anomaly nearby and proceed to investigate. While scanning the second anomaly the Yamato suddenly finds itself caught by an unknown phenomenon and pulled inside the anomaly.
Shortly after starting the scan of a anomaly the Yamato found itself under intense pressure and buffeting as it was pulled along through an unknown form of subspace or extradimensional phenomenon. The crew races to understand what is happening and prevent the Yamato from suffering the same fate as the science vessel Korolev. Unknown forces strike the ship, causing damage to multiple systems. Engineering does an emergency shutdown on the warp core to prevent it from suffering a breach as the Yamato continues to be rocked. When the ship is finally ejected from the phenomenon the ship has suffered severe damage. The main and auxiliary bridges are offline so Chief Engineer sets up an emergency control center in the Secondary Hull. Damage control teams are dispatched as efforts are made to contact anyone in the Saucer Section. It is discovered that the Main Bridge suffered a hull breach, killing Helm Officer Lt. Nayar and the First Officer, Commander Cartwright, who had managed to get Captain Sloane, Science Officer Chen and Communications Officer Lt. Zandr into the turbolift where they were alive but now trapped until power and access could be restored. Similarly the Auxiliary Bridge had been badly damaged and the backup crew there had all been killed. With the sensors also badly damaged a shuttle is sent out to assess the exterior damage, and reveals additional hull breaches in the Saucer Section as well as extensive damage to the warp nacelles. Slowly the Saucer Section is brought online, and once the long-range sensors are at least partially restored the crew are able to get a fix on their location. Shockingly the strange phenomenon has somehow transported the Yamato to the Small Magellanic Cloud, a satellite galaxy of the Milky Way more than 200,000 light years from Federation space.
Over the course of several days the crew of the Yamato slowly tries to repair many of the key systems. The main reactor is brought back online, followed by long range sensors while efforts to fix the damage to the warp nacelles. While waiting for the warp drive to come back online Captain Sloane dispatches shuttlecraft to gather information about the Yamato's new surroundings. Delta 5 take one shuttle to a nearby system with a Sol-type star in case there is an M-class world that could help with supplies. The system turns out to be a failed binary, with a huge super-Jupiter gas giant in a close orbit. At first pass the team does not find any Class M worlds, or any terrestrial worlds at all. Closer examination of an asteroid field at roughly 1 AU from the star reveals that it is the remains of a terrestrial world. On a larger chunk there is evidence that the world had once been inhabited, with the remains of cities. After more detailed scans the team discovers a relatively intact structure that would have been a reinforced underground bunker before the planet broke up. Though anyone inside would have been dead millennia earlier, the possibility of information surviving was not insignificant. Delta 5 carefully gain access to the structure and are able recover ancient paper records, bodies of the reptilian centaur-like beings that once inhabited the planet, and even surviving computer equipment. Back at the Yamato, examination of the recovered artifacts reveals some details of the last days of the dead world. The world had apparently reached a technological level comparable to mid-20th Century Earth, with the bare beginnings of a space program, and had been on the verge of a global conflict between major power blocs when it came under attack by an unknown enemy from space. According to the recovered records, this enemy fired world killer weapons that burrowed into the planet's surface and tore it apart, killing everyone. Those in the bunker only survived for a short time as it was designed to survive bombings, not the planet being destroyed under them. The destruction appeared to have occurred millennia earlier, on the order of 100,000 years ago or so. Even though much time has passed, Captain Sloane is worried these planet destroyers may still be around and thus be a potential threat to the Yamato while they search for a way home.
Sufficient repairs have been made to the Yamato to engage the warp drive. With the nearby systems partially explored by probes and shuttlecraft, the Yamato heads to one of potential interest. The Yamato arrives in the system, another failed binary with a huge super-Jupiter gas giant. Initially there is no indication of any Class M worlds, but probes reveal that a Class Y (Demon) hostile planet shows signs of once being habitable, and inhabited. Though the atmosphere is toxic, there are signs of the remains of cities. Once again Delta 5 is assigned to explore, and they beam down with environment suits and pattern enhancers to enable return transport to the ship. The group split into three teams to explore different parts of the buried ruins. The first team finds several hollow pockets in the earth filling the buried building they are exploring, pockets containing skeletal remains and some surviving artifacts; the second team finds that the pyramid contains the fossilized remains of various types of plants; and the third team finds many fossilized skeletons of humanoids along with a disturbing non-humanoid statue. After some close calls the teams manage to return to the beam out point and return to the ship with their findings. Careful analysis finds that the civilization was pre-industrial, probably a centralized empire of some kind. The explained the survival of the larger more important buildings the team was able to explore as they had been built as impressive megastructures. The major discovery was that everything on the planet appeared to have been killed at approximately the same time, and not just the people but the animals and plants and likely even the more primitive forms of life. The cause could not be determined, as there was no evidence of any known phenomenon. Analysis of the writing found at the base of the unusual statue as well as other clues points to a connection with the ancient "Great Old One" creatures that apparently threatened intelligent life in the Milky Way galaxy millions of years ago. Seeking more information about the potential for these entities to be present in the Small Magellanic Cloud, Captain Sloane orders probes sent out to nearby systems to see if any others show signs of destroyed civilizations. One probe finds a Class M world with primitive inhabitants so the Yamato heads there. While the Yamato is completing its survey in orbit the sensors detect a subspace signal. Investigating a probe of some kind is detected in orbit. It self-destructs as the Yamato approaches, but enough debris is recovered to identify the probe as being Romulan.
Based on analysis of the destroyed Romulan probe as well as the Yamato crew's own knowledge of the Romulans several probes are sent to other nearby systems to find signs of a Romulan presence. One probe finds readings indicative that a cloaked vessel may be operating in the area, so Captain Sloane sends a subspace message via the probe. They receive a reply and are surprised to discover that not only is there a Romulan ship also present here in the Small Magellanic Cloud, but it is a familiar one as the responder is Commander Sheva, captain of a Romulan Bird of Prey that the Yamato had encountered previously. Sheva is equally surprised to learn the Yamato is here and extends an invitation for the Starfleet vessel to join her ship at their current location. Captain Sloane agrees and, with some precautions in place, brings the Yamato to the star system the probe found the Romulans in. When the Yamato arrives a Romulan Bird of Prey decloaks and sensor scans confirm it is the same one they had encountered before. Captain Sloane invites Commander Sheva to come over to the Yamato so they can exchange information. Sheva agrees and beams over with one of her senior officers, Subcommander H'dayn. The two captains agree to exchange information, and Sloane has Lt. Drake send over the scientific data they have collected so far, though instructs him not to mention their theories concerning the “Great Old Ones”. The data from the Romulans in turn reveals that they arrived here several months before the Yamato, but that they arrived by the same manner. Captain Sloane politely avoids bringing up the fact that this meant the Sheva's vessel had to have been very far from Romulan space in order to have been pulled from the same sector of the Beta Quadrant as the Yamato. The discussions continue, but are interrupted by a call from the bridge informing Captain Sloane that one of their other long range probes has detected an unknown warp signature in another star system. Captain Sloane and Commander Sheva agree that both their vessels will head to the system to investigate.
The USS Yamato and their unlikely allies in the Romulan Bird-of-Prey Sacred Blade pursue another warp signature. To facilitate cooperation between the vessels each has sent a liaison to the other, with the Romulan liaison on the Yamato being a female Centurion named Pathauna. There is no sign of a vessel in the system where the warp signature had been detected, but scans reveal the residue of what appears to have been a subspace vortex. They are able to track the vortex to another system, but decide to send a shuttlecraft ahead so as not to frighten the suspected other vessel and the two starships would follow shortly behind. Delta 5, along with Pathauna, take a shuttlecraft and arrive in system but can find no trace of another vessel, but also no sign of another vortex that would indicate the vessel had left. Exploring the system the shuttle finds an unusual binary asteroid pair partially covered in a strange resin-like material. The shuttle comes under attack as tendrils of resin from the larger asteroid try to grapple them. They realize that the smaller asteroid is actually a spacecraft that has been enveloped by the resin. Using the shuttle's phasers Delta 5 are able to break away some of the resin and expose the hull of the trapped vessel. Several of Delta 5 along with the Romulan Pathauna are able to board the vessel while the shuttle continues to use its phasers to break more of the resin away. On board they find the crew of the vessel under siege by large, scorpion-like creatures. The shuttle succeeds in freeing the ship from the resin while the team onboard stop the last of the creatures. The Yamato and the Sacred Blade arrive in system a short time later and are able to offer assistance to the alien vessel. The aliens call themselves the Valoh and reveal that, like the Yamato and Blade, they are not native to the Small Magellanic Cloud and were pulled here by the unknown phenomenon from their home in a Globular Cluster. The Valoh also reveal that there are several other ships similarly trapped and they have banded together in an alliance.
With their vessel repaired the Varoh leave to inform their allies of the arrival of two more lost ships in the region, telling the Yamato and the Sacred Blade they will contact them shortly. True to their word the Valoh return a short time later with word that the rest of what they and their allies somewhat ironically as the Intergalactic Alliance will meet with the two new vessels. The Yamato and the Blade travel to coordinates provided by the Valoh and arrive in what initially appears to be empty space but soon discover there is a large space station there. Scans show that the space station appears to be a somewhat haphazard assembly of hundreds of different spacecraft that measures approximately 3 km in diameter across its shortest axis and 7 km along the longest. A few spacecraft are operating in the vicinity of the station, while some are docked to parts of the exterior; the majority of the rest seem to be derelict hulks centuries or millennia old, all joined together with improvised connections. Captain Sloane and Commander Sheva are invited to meet with the leadership council of the Intergalactic Alliance onboard the station where they learn of the five other members of the Alliance, though only representatives of five of the six total are there to greet them, the sixth they are told are often uninterested in participating in joint Alliance activities. All six members represent the crews of starships that have become trapped in the Small Magellanic Cloud relatively recently, and all under circumstances similar to how the Yamato and Sacred Blade came here. The space station is called Haven and has been here longer than any of them. From what they have learned, whatever phenomenon trapped all of them here has been active for many millennia at least and seems to occur in cycles. The Haven was built by the crew of ship or ships during a much earlier cycle and has been added to by more crews over subsequent cycles. The implication of this is that none of the ships ever found a way back to their homes, which does not bode well for this latest group, but the Alliance holds out hope that by working together they may yet find a way. By agreement of the members of the Alliance both the Yamato and the Sacred Blade are invited to join the Alliance, and both captains agree. When Delta 5 learn that the older interior of the Haven has not yet been explored in depth by any of the Alliance the team volunteers to undertake this task while the Yamato is exchanging scientific data with the other members of the Alliance. The team explore a section from what appears to be one of the earlier cycles. They pick separate areas made up of three different ships, noting the efforts made to interconnect power and life support systems between radically different technologies. One of the three appeared to have served as a central gathering area for an ancestor of the Intergalactic Alliance. Some material with writing has survived so the team scans it for later analysis but the larger question is, if these people never returned home then where are all the bodies?
Delta 5 embarks on another expedition deeper into the depths of the Haven, examining another trio of vessels. One is very spartan, with frequent repeating, sparse utilitarian control stations and a low level radio field everywhere. The second is almost extravagant, with frequent carvings and statues molded by some unknown technology. Some of the statues hint at a mutli-species alliance, with three distinct, unfamiliar alien races depicted along with three different kinds of writing. The third ship is the most primitive of the three, with technology roughly a century behind current Federation standards, but onboard Delta 5 find an important artifact, a sheet of metal that does not match the material from the vessel and must have come from an even earlier generation of Haven occupants. Importantly, the metal sheet has carvings of symbols in multiple languages, but one of the symbol sets match those found on fragments of ancient papers found in one of the more recent generation of vessels. Could these symbols represent an earlier attempt at a common written language? After returning with their findings Delta 5 hand over the metal sheet to the Science division for closer examination and decide to pursue other avenues of investigation. Based on the fact that none of the vessels of any of the Haven generations they have examined so far show signs of violence breaking out between the diverse species inhabiting Haven at the time, Armitage wonders if there is an outside influence helping to maintain the peace. He reviews the psycho-logical records and personnel logs on the Yamato, comparing the period prior to the ship's arrival here to the present looking for any unexplained shift in behavior, but his findings are inconclusive. Wondering if any ships ever left Haven and tried to settle on worlds in other star systems, Ensigns Deelo, Vasquez, Jacob and Sharad take a long-range shuttle and start surveying nearby systems to look for evidence. Their first stop is a trinary star system, but they don't turn anything up so return to the Haven to prepare to report and resupply before they head to the next target. Other members of the team decide to investigate the Tintantin, the most reclusive and mysterious members of the Intergalactic Alliance at Haven. Sevek and S'Chal contact the Tintantin to try direct negotiations, while Lt. Drake attempts a more covert investigation alongside the Romulan Centurion Pathauna. Sevek and S'Chal's effort makes little progress, other than revealing that the Tintantin have very alien thought processes that makes getting any answers from them extremely difficult. Drake and Pathauna opt to make an EVA to examine the Tintantin section of Haven from the outside. There they observer bio-organic components of the ship, including a large flower-like structure that seems to serve as a sensor and/or communications array and large beetle-like creatures that act as maintenance bots, feeding and tending to the flower-arrays.
Efforts to locate vessels from earlier eras that left or never joined the Haven pay off when a long-range probe investigating a spatial anomaly in one of the target star systems reported sighting what might have been a derelict space vessel shortly before contact with the probe was lost. Lt. Drake assembles a team made up of members of Delta-5 as well as representatives from the Valoh, Thonnu, Q'Hari and Romulan vessels to take the long-range shuttle Sojourner to investigate the loss of the probe and report on any discoveries. The anomaly is revealed to be a four-dimensional fracturing of space with the derelict at its center. With some effort the shuttlecraft traverses the anomaly and successfully docks with the derelict spacecraft at the center of the distortion. The derelict is several millennia old, giving off no life or power readings, and its hull is shaped roughly like a long-necked bird, with a forward command module connected to an engineering hull by a reinforced corridor that includes the airlock the shuttle has connected to. The engineering hull had two large wings mounted port and starboard with impulse engines mounted close to the hull and warp nacelles on the ends. The exploration team dons environment suits and enters the derelict through the airlock. Half the team heads forwards to the command module while the other half heads aft to engineering. In engineering the team finds that something has rendered the remaining matter and anti-matter fuel inert, but they are able to get the ship's battery power online enough to turn on the lights. The team in the forward section find the remains of the crew, apparently having killed each other in brutal fashion. Computer records also appear to have been wiped, though some data is recovered. The engineering team discovers the main shuttlebay has been turned into an experimental propulsion system that the recovered data calls a Tesseract Drive. Usage of the drive apparently made a connection to the realm of the Elder Things and drove some of the crew insane, leading to the battle that killed everyone on board. The original crew had been telepathic and their death left a psychic taint on the vessel that started to affect the telepathic members of the exploration team. Rather than risk the safety of the team Lt. Drake orders everyone back to the shuttle but they discover its fuel has also been rendered inert. Some deuterium is recovered from the derelict's tanks, but the Valoh Technician Zula succumbs to the psychic taint and tries to replicate the functions of the Tesseract Drive with the derelict's warp drive, leading to a psychic assault from the Elder Things. S'Chal is able to block the assault long enough for the warp drive to be shut down. With the shuttle partially refuelled the team leaves, with Deelo bringing components salvaged from the Tesseract Drive. Leftover deuterium from the derelict that leaked out during the fuel transfer is ignited, causing an explosion that destroys the derelict as the shuttle escapes. The Yamato retrieves the shuttle and the team, while Zula reveals the telepathic attack from the Elder Things included directives to "Kill the Oracle" and "Burn the Haven", indicating they were at least somewhat aware of who the team were and where they were based and raising the question of who or what is the Oracle.
Information inferred by the "Rosetta Stone" discovery from exploration of the Haven and analysis of scans of the Tintantin indicates that the reclusive insectoids may have been present at the Haven for far longer than originally believed. A second attempt by the Yamato crew at communicating with them, including inquiring about the mysterious Oracle that Delta 5 learned about, has prompted a new reaction from the Tintantin; the nature of which has not yet been revealed. Meanwhile Deelo, with Vasquez's help, has been using his Starship Simulator to try and replicate the 4-dimensional effects encountered on the recent mission to an ancient derelict vessel. The effort has unforeseen consequences when, despite it being a simulation, the use of the subspace field equations from the derelict still generates a connection to the Elder Things that starts to have an effect on Vasquez as well as the physical environment of the simulator. Deelo shuts the simulator down immediately and gets Vasquez to Dr. Armitage for examination. Based on the pair's description of events, Armitage worries that the connection might have also affected the ship's computer and alerts Chief Engineer Kaar-Ares. The concern turns out to be accurate and Lt. Cmdr. Kaar-Ares works to isolate key ship's systems from computer control. Kaar-Ares and Deelo must rush to the scene when the infected (or perhaps possessed) computer tries to interfere with transporter operations as Sevek and S'Chal are being beamed back aboard from the Haven. They successfully cut the computer out of the transporter in time to save the duo beaming aboard, and then finish severing the computer's higher functions from ship's systems. Dr. Armitage attempts to psychoanalyze the computer to discover the extent of the damage. It becomes clear that the Elder Things had been able to use the connection to program the computer with new primary directives. Unable to get far in his interrogation, Armitage calls in Sevek to help. Using his Kolinahr-enhanced logic and in-depth knowledge of Starfleet protocols, Sevek traps the computer in paradox by getting it to try and reconcile the new directives with its original programming. Unfortunately this results in the higher logic circuits in the computer core burning out. As repairs proceed on the computer core, the Tintantin summon the Council of the Intergalactic Alliance. At the Council Chambers on Haven, a quartet of Tintantin beetles arrives carrying a pulsating cocoon that appears to be holding a humanoid figure. The beetles deposit the cocoon and leave as the figure in the cocoon tears its way free. The being is a humanoid female with green, chitinous skin, segmented insectoid eyes and antenna. She introduces herself as the Scion, gestated by the Tintantin as a response to the imminent arrival of "The Enemy". The Scion is able to answer some of the Alliance's questions, and when asked about the mysterious Oracle she indicates that the Oracle can be found in the Heart of the Haven and that she can guide the Council to them.
The newly revived Tintantin Scion readies to lead a group made up of volunteers from each of the ships at Haven, with members of Delta 5 going on behalf of the USS Yamato, down to the lower levels of Haven to find the Oracle. When questioned of what to expect, the Scion indicated that she could not say due to the time that had passed since her predecessor had last made the trek down, though was confident of finding what the sought because she could "still hear the message". After reaching the lowest level explored so far, the group set up a base camp, leaving some volunteers behind to help relay communications and act as a backup. The trek deeper into Haven is dangerous; one ancient, primitive derelict spacecraft the group passes through has become so unstable that sections of corridor collapse under them, leading to several injuries, including fatal ones for one member of the Valoh party. The remaining volunteers press on, encountering another derelict that has been overrun with fungal life, necessitating everyone using life support gear to safely traverse the "fungal jungle". Deeper in S'Chal begins to hear the telepathic message the Scion mentioned, a message that apparently relates the story of the original alliance that battled the Elder Things. Dr. Armitage believes that everyone at Haven may have been hearing the message subliminally, which may explain why there is little evidence of conflict among later groups that have inhabited Haven, including the present Intergalactic Alliance. After establishing more base camps, the remaining group is nearly stopped by a crystalline web barrier that threatened to cook them alive with redirected and amplified infrared radiation. Successfully bypassing this they reach a section of Haven that is more than half-a-million years old, a section that the Scion indicates is the location of the Oracle. The Oracle is revealed to be an Arretan named Arrakesh, the last surviving member of the crew of a ship that came to Haven 600,000 years ago who has preserved his consciousness in an Arretan receptacle down through the ages. Arrakesh makes telepathic contact with the group and to facilitate interaction one of them is asked to volunteer as a host. Having learned that the ancient Arretans are related to Vulcans, and therefore Romulans, it is Centurion Vajan, one of the Romulans in the group, who offers his body. Vajan's consciousness is transferred into the receptacle, allowing Arrakesh to take possession of his body. Arrakesh then accompanies the group back up through the levels of Haven where he is brought before the Alliance council. Arrakesh is able to answer many questions based on having experienced nearly a dozen separate incursions by the Elder Things over the millennia since he and his crewmates first became trapped in the Small Magellanic Cloud.
Among the revelations from Arrakesh, the Oracle of Haven, was that the arrival of the Elder Things is pre-ceded by the appearance of Harbingers. The Harbingers are attack craft that are often found on or near worlds that are under the psychic influence of the Elder Things. Based on this and other information from Arrakesh, the Alliance starts sending ships out to look for signs of the Elder Things' presence. The Na-Kesh scout vessel Starhunter is conducting reconnaissance of systems to identify inhabited worlds that may be under the influence of, or at least potential targets of, the Elder Things. They are orbiting a world that is home to a primitive society where there is evidence of Elder Thing worship when an unidentified vessel starts to close with them after emerging from the planet's shadow. Sensors had not registered the vessel entering the system and there was no warp signature so it must have originated from the planet itself. While not familiar to the Na-Zek, the vessel's appearance is close enough to Arrakesh's descriptions for them to believe it to be a Harbinger, and the vessel immediately launches an attack against the Starhunter. The Na-Zek are able to score some lucky hits against the Harbinger and flee the system in order to warn Haven. When Haven receives the distress call the USS Yamato heads to intercept the Starhunter, which reports that the Harbinger is pursuing them and that they have detected the approach of a second one. As the Yamato approaches they detect that the Starhunter has been pulled out of warp, which Lt. Drake deduces to be due to the Harbingers presence distorting local space-time. The Yamato arrives as the two Harbingers are attacking the Starhunter, which has lost its shields under the assault. The Yamato engages, drawing one of the Harbingers away. After a back-and-forth battle the Yamato has sustained some damage, but has at least momentarily immobilized the Harbinger. By this point the second Harbinger has dealt more damage to the Starhunter, so rather than risk both ships Capt. Sloane orders the crew of the crippled Starhunter be beamed over to the Yamato and then goes to warp. After pushing the engines the Yamato is able to escape the pursuing Harbingers and then makes its way back to Haven with the surviving Na-Zek.
While the Yamato undergoes repair of the damage from the encounter with the Harbingers, Capt. Sloane authorizes Lieutenants Drake and Sevek to organize a mission to find the original core of Haven. In addition to members of Delta Five, the team they assemble includes the Romulan Centurion Pathauna, Na-Zek Science Officer Royah Verat, Thonnu medical specialist Bzut Bobboblin, and the Q'Hari Lieutenant Ke'oria Trejan. After reaching the lowest level explored so far, the Oracle chamber, the team begins their trek. With Lt. S'Chals' abilities, the team would attempt to find the source of the telepathic message described by the Tintantin Scion. With that giving them a direction of travel, the team began navigating through the successive layers of wrecks towards the core. As they progress, the team passes through some wrecks that still have power, either internal or originating from an external source, despite the vessels being over one million years old in some instances. In one case the team had to fight and evade what appeared to be custodian robots still protecting one long derelict vessel. Another ancient vessel was infested with Denevan Neural Parasites, forcing the team to defend themselves long enough to make it through. Deeper into Haven the team notice a growing force of gravity, one increasing at such a gradient as to require a powerful artificial gravity generator or a hyperdense source like the core of a neutron star at the center of Haven.
From one of the last derelicts, after descending about 500 meters more or less straight "down", the team unexpectedly emerges on an uneven rocky surface. Gravity here is approximately 0.35 G, roughly the equivalent of Mars gravity. A low-lying mist obscures visibility and the team are assaulted by what appear to be mobile corpses of various alien species. Phasers have little effect, but tricorder scans show that the bodies are being preserved and animated by a fungus of some kind. The team are then able to drive off the creatures using chemicals from their medical gear. The team's security escort is lost when he falls through the unstable surface, but this also reveals ways further down. Continuing to follow the telepathic signal, the team finds the outer shell of a buried structure where someone has installed a manual hatch. Down inside they find that the structure is part of a larger installation, the original that was a series of interconnected spherical station orbiting a neutron star at the optimum distance that the force of gravity in the stations was an average of approximately 1G. The station has been heavily salvaged over the millennia by generations of newcomers to Haven, but in a large auditorium the team finds the original telepathic broadcast message, the story of the original galactic alliance of the Milky Way that established the transwarp conduit network that drew the current Alliance's vessels to the Small Magellanic Cloud and how they left this installation as a watchtower against the inevitable return of the Elder Things as they retreated back to the Milky Way and established the Galactic Barrier. The team also finds additional records on the transwarp network, providing potential clues to ways for the Alliance members to get home.
The Yamato's Science and Engineering divisions lead Alliance efforts to analyze all the data brought back from the core of Haven. Based on the new understanding of the ancient transwarp conduit network, they theorize it might be possible to locate the exit and entrance points of the network. To facilitate this, Delta Five proposes salvage of the Na-Zek vessel destroyed by the Harbingers, as that ship had the kind of advanced sensors that would help the search. The effort is successful, with the salvage team managing to evade another Harbinger attack. At Haven, the Romulan Bird-of-Prey returns from a patrol with news of several worlds being recently destroyed, apparently heralding the full arrival of the Elder Things. Examining the data, Lt. Drake and his team theorize that the enemy is entering from four-dimensional space and that it may be possible to track where the next target system will be. To assist with the efforts, Lt. Armitage gets the Thonnu Doctor Bzut Bobboblin to heal the Yamato's Chief Science Officer, who has been comatose since the Yamato first arrived in the Small Magellanic Cloud and has expertise that could help. The surgery is successful, and to gather data the salvaged Na-Zek sensors are installed on the Arcurian's vessel.
The Yamato and the Romulan Sacred Blade are scouting out the potential target systems for the next Elder Thing Incursion. The Yamato finds an inhabited M-Class world orbiting a Sun-type star, and orbital scans find an Outside Harbinger craft on the surface. The Yamato retreats to the system's asteroid belt to evade detection and continues observation. S'Chal attempts a telepathic scan but as soon as his defenses lower he detects an oppressive sensation. Soon the ship's sensors detect a massive subspace disturbance in the outer system, followed by a variable gravitational force. To protect the ship from the growing oppressive psychic force, controls are locked to the Yamato's bridge where the command crew can be protected while the rest of the crew is carefully monitored. The Incursion manifests as a massive 4-dimensional object intersecting with 3-D spacetime. As only a portion of the object is present at any given instant, it appears to vary in size radically from moment to moment. This also changes the mass of the object relative to spacetime, resulting in gravitational distortions as it shifts from the size of a small moon to an Earth-size planet or greater. Visually, the object varies in shape, being very irregular and constantly shifting continuously. The Yamato stays in system as long as possible before it becomes clear that either the crew will succumb to the telepathic assault or the ship will be detected. They flee the system before either can occur, leaving behind a probe that is soon discovered and destroyed by a Harbinger. The Yamato then returns to Haven with the trove of data they have collected on the Incursion.
The Yamato has witnessed an Incursion and escaped with valuable data from the encounter. The Alliance is analyzing the data seeing if there is a way to defend against the Enemy, or possibly even go on the offensive. At the same time, Dr. Armitage leads a team examining the physiological and psychological effects of being in the presence of the Elder Things, to see if there are ways to protect the Alliance members. They are able to categorize which psychological profiles are more vulnerable than others, allowing crews to be selected along those lines for future missions. The examination of the Incursion data itself reveals the possibility of disrupting the four-dimensional interface. After conducting simulations, they find that there is an opportunity to not only block an Incursion, but to completely block any future attempts, at least for this cycle. The Alliance members come up with a plan to stop the Elder Thing Incursions, one requiring all the surviving Alliance space vessels. The plan will require the vessels to engage during an actual Incursion, using the sensor readings of the Incursion itself to feed a subspace manipulator to counteract and ultimately disrupt the Elder Things' four-dimensional interface. The key elements are the Valoh ship, which has electromagnetic projectors they use to generate subspace tunnel for warp travel; and the Arcurian ship, which has the Na-Zek sensor array installed, and can also play host to the Gith, who would be required to make the necessary calculations based on the sensor readings quickly enough for the Valoh ship to make use of them. Since any action would take time, the Yamato and the Romulan Bird-of-Prey will be tasked with protecting the Valoh ship until the interface is fully disrupted.
When the location of the next Incursion is determined the plan is put into motion. To help protect the crew of the Romulan Bird-of-Prey, Lt. Sevek performs Vulcan mind melds with the ship's senior officers to temporarily share his Kolinahr mental discipline. Sevek then joins the crew of the Valoh vessel, where he can similarly share his mental strength through the Valoh's own telepathic powers. Lt. Dawnslight also comes aboard the Valoh vessel so he can help modify their subspace manipulator to disrupt the interface. The Yamato's senior officers are to be protected by Lt. S'Chal and his ability to generate telepathic interference. With the Na-Zek sensors, the Arcurian vessel can remain far enough away to be safe from retaliation. The Thonnu vessel is kept in reserve to serve as a rescue vessel. Once the Incursion begins and the enemy realizes the threat the Valoh ship represents several Harbinger craft are dispatched, but the Yamato and the Romulans are able to successfully hold them off. The plan succeeds, though the Valoh vessel is lost in the process. The Incursion is stopped, and the four-dimensional interface permanently disrupted. Some Harbinger craft remain in the Small Magellanic Cloud, but they present a much lesser threat, being no longer able to interact with their Elder Thing masters. The Valoh are successfully evacuated to the Thonnu vessel and the surviving Alliance ships return to Haven to celebrate their victory.
Against all odds, the Enemy has been driven back to its home in the upper dimensions. With the threat gone, the members of the Alliance at Haven now turn their attention to the task of getting home. Deelo is temporarily transferred to the Sciences division and assigned to help Chief Science Office Chen with his research into the intergalactic transit network. While this is happening, Capt. Sloane and Lt. Sevek are negotiating with the other Alliance members to decide on a common direction and get assistance with the work on the research. After weeks of work several theoretical models of the interstellar transit network are ready for testing and teams from multiple Alliance vessels search for the entry and exit points predicted by the models. Several exit nodes are identified, including one that appears to connect to the Large Magellanic Cloud, home to the Arcurians. No tunnels appear to connect to the Milky Way, seeming to confirm that the original builders had cut off the return routes in order to protect the galaxy from the Elder Things. Some tunnels do seem to connect to extra-galactic space, indicating they end just outside the Galactic Barrier. With the tunnels confirmed, the Alliance members make their decisions. The Tintantin are remaining behind, as Haven has been their home for millennia, and the Q'Hari similarly decide to stay to maintain Haven and ensure that future travelers will know how the Elder Things were defeated. They will give the Yamato messages to send and the communications protocols necessary to send them to their territory in the Alpha Quadrant. Without their ship, the Valoh have no way to return to their Globular Cluster, but the Arcurians offer to take them with them to the Large Magellanic Cloud and to help them try to return home from there. The Yamato, the Romulans and the Thonnu plan to use the partial tunnel to reach the outskirts of the Milky Way and then attempt to get through the Galactic Barrier. Also lacking a vessel, the Na-Zek are welcomed aboard the Yamato, who offer the Federation's help to get them to their home in the Alpha Quadrant should their effort succeed.
The Arcurians are the first to leave, taking the Valoh with them as promised, with the Yamato assisting in activating the tunnel to the Large Magellanic Cloud. After the Arcurian ship enters the tunnel, the Yamato waits in suspense until they receive a message confirming success. The Arcurian message also contains detailed scans of their transit through the tunnel, data that will help the others in their attempt. Thanks to Valoh magnetic containment technology, Na-Zek subspace field equations, Gith n-dimensional computations, and Starfleet engineering expertise, the USS Yamato's warp drive is upgraded to new levels of power and efficiency. The ship is ready to take the point on the risky journey back to the edge of the Milky Way, and through the Galactic Barrier. It is determined that the Romulan Bird-of-Prey is the most at risk, but thanks to its smaller size it is decided to anchor the Sacred Blade to the much larger Thonnu vessel, the Trailblazer. The Yamato takes the lead as the faster and more maneuverable ship, with the Thonnu slaving their vessel's helm to follow the Yamato's course through the tunnel. Both ships' warp cores are put in standby modes to minimize tachyon buildup that might cause a breach and they send the signal to activate the tunnel, and then enter at impulse speeds. It is a rough ride, but Vasquez is able to navigate the tunnel well enough to minimize damage to both vessels despite the stresses of the journey. At the other end the vessels are spit out of the transwarp tunnel. The Yamato's improved warp code is run up to maximum and power sent to the modified warp drive. The ships attempt to capture as much of the tunnel's enhanced subspace field as possible, synchronizing it with the Thonnu's warp field and in turn with the Yamato's before pointing the Yamato towards the Milky Way and accelerating to maximum warp. With the enhancements the Yamato goes well beyond its previous maximum safe speed and hits Warp 9.5 before hitting the Galactic Barrier. It is close, with ship's systems strained to the limit, but the ships punch through the Galactic Barrier, travelling hundreds of light years almost on momentum before the subspace fields decay enough to bring them all out of warp. After assessing the damage and confirming the Thonnu and Romulans have made the trip intact, the Yamato's astronavigation team is able to identify NGC 5139, Omega Centauri, the largest Globular Cluster inside the Milky Way. From it they are able to calculate their current position as being at far end of the Beta Quadrant, in the Carina Arm, almost 40,000 light years from the Federation and nearly 7,000 light years from the border between the Beta and Delta Quadrants. While far from Federation space, the three ships are relatively closer to Thonnu space, which lies in the Delta Quadrant just over the border with the Beta Quadrant. The Trailblazer sends a signal towards their territory, and after a few days receive a response from a Thonnu exploratory fleet. The Thonnu offer the assistance of the fleet, even though rendezvousing with them will take the Yamato and the Romulans in the wrong direction.
The Thonnu have made contact with one of their deep space exploration fleets and have offered to provide assistance to the Yamato and the Romulans. Both agree to the proposal, a few dozen light years in the wrong direction is not much given the thousands of light years that still stand between them and the Alpha Quadrant. As the trio approach the rendezvous coordinates, the Thonnu receive a distress call from the exploration fleet indicating they are under attack by an unknown adversary. The three ships race to the location, and when the attacking vessels detect their approach they break off the attack. The Trailblazer contacts the exploratory fleet and learns that the unknown attacker had boarded the fleet and taken several of the crew captive before fleeing. The Trailblazer remains behind to assist the fleet and the Yamato and the Romulans head off in pursuit of the attackers, with Dr. Bzut Bobboblin beaming over to the Yamato to help with the rescue attempt. As the faster ship, the Yamato catches up with the two attacking vessels first. There is no response to hails, and the two ships move into an attack formation. The Yamato engages them, discovering that the enemy has an unknown weapon that is capable of dampen-ing a ship's power systems. After a tense battle, one mystery ship has been temporarily disabled, but not before it was able to nearly cripple the Yamato with its power-draining weapon. With the Romulans still too far out to help, Capt. Sloane orders a boarding party to take a shuttle to the remaining enemy vessel in an effort to locate and beam out the Thonnu captives before that ship can turn its full attention back to the Yamato. Delta Five takes the mission, accompanied by Bzut Bobboblin, using the Pathfinder shuttlecraft. Using phasers to weaken a portion of the enemy hull, the Pathfinder rams through to get aboard. Once inside the teams get a reading on Thonnu biological signs coming from two locations in the forward section of the ship, so the team splits up. At the site of the stronger signal the first team locates most of the Thonnu in a holding pen. They fight off five of the enemy, unknown aliens with vicious fighting skills, and free the Thonnu prisoners and tagging them with transponders to aid transporting them back to the Yamato. The other team finds a trophy room and discover that the Thonnu there were dead, the readings coming from one Thonnu's skeleton and another whose body was being processed in some strange vat. The team notice that among the trophies is a bat'leth and a Klingon skull, meaning these aliens must have encountered Klingons. They hack the ship's computers and download any data related to the Klingon encounter before engaging in a firefight with the ship's senior officers. Once the data is recovered the transponders are activated. The enemy ship had activated a scattering field, but the Yamato is still able to get a transporter lock and beam everyone safely back. The shuttlecraft is detonated to prevent the enemy from learning anything and to provide an additional distraction to delay or deter pursuit. Having partially restored power, the Yamato is able to jump to warp and meet up with the Romulans. The enemy vessels opt to lick their wounds and not prefer, allowing the Yamato and the Romulans to rejoin the Thonnu fleet with the rescued crew.
Analysis of the navigational data that Delta Five pulled from the hunter ship leads the Yamato to a resource-rich star system with one Class M planet. The planet is a jungle world, but with no intelligent life. In a decaying orbit above the planet is the wreck of a Klingon scout vessel. The vessel is extensively damaged with no active power or life support and no life signs. A team beams aboard the more intact command pod section and sees evidence of a firefight and melee on the bridge. Once the team has recovered as much data as possible, and after taking as detailed scans as possible of the wreck, the team beamed back to the Yamato to do more analysis. The data shows the Klingons were recent arrivals, encountering some kind of subspace anomaly that pulled them to this region about seven weeks earlier. The event damaged their ship and they made it to this planet but soon found themselves under attack by three alien ships. The Klingons managed to obliterate one of the enemy ships by venting their antimatter fuel, but they were eventually overwhelmed and boarded. The surviving two enemy vessels were the same ones that went on to attack the Thonnu. There is enough data to pinpoint where the Klingons emerged so the Yamato heads to those coordinates, joined by the Romulans. It appears to be a region of empty space but scans show indications that a wormhole had been there, with particle decay analysis giving a time that lines up with the Klingons' arrival. There are no known stable wormholes in the galaxy, so this is likely an unstable one. Based on the latest wormhole research the Yamato's Science division find some theories that wormholes might be attracted by certain types of exotic particles, notably verterons. Members of Delta Five work with the Romulans and are able to successfully convert one of the Yamato's phaser banks into a verteron array. Firing the verteron beam at the region where the wormhole exit was when it pulled the Klingons through causes a subspace distortion to form at the location. Scans show it to be a partially open wormhole, and amongst the data pulled from the interior is a heavily distorted subspace reading that some intense analysis, data repair and transformation work manages to resolve into part of a Federation subspace transmission, a routine routing message. Having ascertained that the wormhole still connected closer to home, the ships determine a way to open and maintain the wormhole long enough for both the Yamato and the Bird of Prey to get through. The Yamato is the bests suited vessel to the task, so once the wormhole opens the Romulans go through first. Sensors monitor their progress, and readings further confirm that the other end of the wormhole still connects to somewhere relatively close to Federation space. The scans also detect that the Romulan traversal of the wormhole has started to destabilize it, forcing the Yamato to enter before it collapses. It is a rough ride, and pushing the reactor nearly causes the dilithium to fuse and crash the whole main power system but the Yamato emerges from the other end of the wormhole before the systems go past the critical stage. A cursory scan shows no sign of the Romulans, but also no indication of debris or other sign of an accident or loss of the vessel. There are strong gravitational, electromagnetic, and gravitational distortions in the area, caused by something other than the wormhole, which makes it difficult to get a fix on any Federation navigation beacons so the astronavigation team have to try and identify the Yamato's position by dead reckoning from visible stars and pulsars. They eventually get a fix on the Yamato's position and confirm that the ship is definitely much closer to home, but unfortunately the wormhole has deposited the ship in the middle of one of the most dangerous regions of space in the Beta Quadrant - the Shackleton Expanse.
As hoped, the wormhole from the Delta Quadrant borderlands has shortened the Yamato's journey home by thousands of light years, though the journey through the wormhole was a rough one and took a toll on the ship's systems. There is no sign of the Romulan Bird-of-Prey that preceded the Yamato through the wormhole, but there is also no immediate evidence of its destruction. Trouble with long-range sensors forced a more old-fashioned method of determining the Yamato's new location, and the results put the ship in the Beta Quadrant, in an area of space known as the Shackleton Expanse. Gravimetric interference makes using long range sensors difficult, but the Yamato determines that the Romulans exited at a different location, as the mouth of the wormhole at this end had moved. Efforts at contacting the Bird-of-Prey eventually succeed. The Romulan commander is pleased that the Yamato survived, but heading to rendezvous with them would take the Sacred Blade further away from Romulan space. Similarly, the Yamato heading to join the Bird of Prey would take them further from Federation space and closer to the Romulan border. It is clear that this is the point at which the two vessels must part ways. Commander Shiva expresses their gratitude, or as close as she can, at the cooperation between the two over the last almost two years, but her first duty is to the Romulan Star Empire. She wishes the Yamato luck on the rest of their journey and the communication ends. With a lack of available astrometrics data it is difficult to know what the best course of action is. Some estimates give the Shackleton Expanse a volume larger than all of Federation or Klingon space. Even the borders are relatively undefined, though in the neutral region of space between the Klingons and the Romulans there is a large body of interstellar gas and dust referred to as the Endurance Divide that is generally considered to mark the beginning of the Expanse in that region. The Yamato is able to detect the rough direction of Federation space and opts to head that way. The trip is long, as they soon discover that moving at too high a speed damages the main engines forcing the ship to stay below Warp 4. They must also contend with the constant electromagnetic and gravimetric eddies prevalent within the Expanse, as well as subspace anomalies. The trek takes its toll on the ship and on her crew, keeping the engineering and support teams on constant alert, and the medical staff on equally high status monitoring the physical and mental condition of the Yamato's crew. After weeks of difficult effort, however, the Yamato eventually reaches the Endurance Divide.
Delta 5, along with shuttle pilot Ens. Jimmy Parker, are using the shuttlecraft Sojourner to scout a path for the Yamato through the Endurance Divide at the edge of the Shackleton Expanse. A subspace shockwave disables the Sojourner's communications and knocks it far off course. Sensors are nearly useless in the Divide, making it nearly impossible to locate the Yamato. Following a faint signal the Sojourner comes across another Federation vessel, the survey vessel USS Ibn Battuta, apparently adrift inside the Divide. Boarding on the vessel through its main shuttlebay, Delta 5 finds no trace of anyone on the lower decks. Ens. Parker disappears without a trace, followed by unknown persons ejecting the Sojourner into space and stranding Delta 5 on board the Inb Battuta. The team finds that the main decks of the saucer section are suffuse with a strange purple mist that causes physiological and psychological reactions on contact. Tricorder readings show anomalous subspace readings on the main decks, but that the upper decks appear to be clear. The team risks a rapid ascent through the Jeffries Tubes only for Ens. Sharad to also disappear in transit.
Repairing systems on the upper decks, Delta 5 pieces together much of what has happened to the Ibn Battuta. While on assignment to deploy subspace relays, the Ibn Battuta was pulled into the Divide and became stranded due to subspace anomalies. Additional unknown effects cause the crew to deteriorate psychologically and they fail to identify a threat harming and later killing several of them until it is too late. Finding a set of environment suits a group consisting of Lt. Drake, Lt. JG S'Chal, Ens. Dawnslight and Ens. Taylor head down to investigate Main Engineering. Ens. Taylor disappears en route, just as Ensigns Parker and Sharad earlier. The remaining three continue on to Engineering, passing one of the secondary shuttle bays and noting that some shuttles still remained. In Engineering, Ens. Dawnslight sees that aliens from subspace manifold have used a subspace rupture to invade the vessel, completely occupying Main Engineering. The aliens spot Ens. Dawnslight and as they converge on him, he uses his phaser to breach one of the impulse reactors, causing a plasma burst to cover his escape before the safeties cut in. Drake reports the situation to Lt. Sevek on the Bridge, who decides their best course of action is to use one of the Ibn Battuta's shuttles to escape and to try and destroy the ship to stop the invasion. Drake, Dawnslight and S'Chal head for the port secondary shuttlebay and take two shuttles, one to evacuate on and one to use to ram one of the Ibn Battuta's nacelle antimatter pods to destroy the ship. Though it requires a short exposure to the vacuum of space, the surviving members of Delta 5 are able to get aboard the shuttlecraft Damascus while the Medina is rigged for remote control. The aliens realize the danger too late, and despite desperate efforts with the ship's tractor beam and phasers they are not able to stop either shuttle. As Delta 5 flee aboard the Damascus, the Medina is sent into the starboard nacelle, rupturing the antimatter pod and destroying the USS Ibn Battuta.
After more than a week aboard the shuttle Damascus, Delta 5 are at last able to cross out of the Endurance Divide and escape the Shackleton Expanse. Hoping to signal the Yamato, still somewhere in the Divide, using a subspace relay salvaged from the USS Ibn Battuta, the shuttle is instead intercepted by the USS Bozeman, a Soyuz-class vessel dispatched by Starfleet to find the missing Ibn Battuta. After being treated for their ordeal on the shuttle, Delta 5 are debriefed by the Bozeman's commanding officer, Capt. Morgan Bateson. The Bozeman is able to use its advanced sensors to locate and contact the Yamato, guiding it out of the Divide. Capt. Sloane meets with Capt. Bateson, exchanging information and sending a message to Starfleet Command. After helping repair the Yamato, the Bozeman accompanies it on the still-lengthy, and dangerous, journey towards Federation space. The trip is interrupted by a distress signal from a Tellarite mining colony and the two vessels respond. The signal is a trap and the ships are ambushed by a trio of Nausicaan raiders, but the Federation vessels cripple one raider and disable the weaponry of another, leading to two of the craft to flee and abandon their crippled comrade. Questioning the captured Nausicaans, it is learned that rumors of the USS Yamato has spread due to leaked intelligence the Klingons picked up from the Romulans. The rumors purport that the Yamato is in possession of advanced extra-galactic technology, which has led groups like the Orion Syndicate and independent fortune seekers to search for the ship as well as both the Romulans and the Klingons. With so many hunters after the Yamato, Capt. Sloane accepts a recommendation from the senior staff to make a run through the frontier Triangle region located at the intersection of Klingon, Romulan, and Federation space; the quickest, but perhaps most dangerous, path to safety.
With a roundabout route home not safe due to the disparate groups all hunting for the Yamato, Capt. Sloane has opted to make a direct run through the volatile region known as the Triangle. To reach the Triangle region proper, the Yamato must first navigate a narrow corridor between Romulan and Klingon space. The crew must bluff their way past a Klingon monitor outpost near the border, but eventually the Yamato enters the Triangle. The ship only makes it a short way before they suffer a major setback when the Yamato's warp reactor fails due to all the recent strain it has been under. The Yamato limps to a nearby system where they can use a gas giant to evade potential detection. To get the warp core back online they need replacement dilithium, so Delta 5 is dispatched on a mission to the relatively close New Paradise colony. While the colony is mostly human, it is independent and there is both a Klingon and Romulan presence on the world, necessitating that the team adopt a cover story, choosing to pass as pilgrims from the Wanderer cult that the Yamato had encountered some years earlier. Using the shuttle-craft from the USS Ibn Battuta, further disguised to appear to be Federation surplus, the team lands at the spaceport outside New Paradise's capital city. Some inquiries at spaceport recreation facilities lead the team to an Orion who can provide them with some dilithium. Lt. Drake and the Na-Zek security officer Grimma split from the team for reasons Drake cannot disclose, leaving the others to meet with the Orion. They have a close call with some possible Romulan intelligence agents, but their cover remains intact and they are able to trade with the Orion for the dilithium. It is not an ideal amount or quality, but Ens. Dawnslight believes it will be sufficient to get the Yamato out of the Triangle and into Federation space. As the team returns to the shuttle they notice a heightened level of security at the spaceport and Lt. S'Chal must use his telepathic abilities to get them past an inspection team. Drake and a wounded Grim-ma are waiting for them at the shuttle, but do not provide any details on what they had been doing while the team was getting the dilithium. After nearly five years together, the members of Delta 5 know enough to not ask too many questions and they leave with the dilithium crystals and return to the Yamato.
With the replacement dilithium installed the USS Yamato resumed her journey homeward. Now, after having traversed much of the Triangle region undisturbed, the Yamato receives warning from Starfleet Command that those hunting the vessel have learned of her location. Under orders from Admiral Nogura, Starfleet has launched a fleet of its own from Starbase 24, but it will not reach the Yamato before the hunters do. One option Captain Sloane considers is to use the Azure Nebula to evade the pursuers. Even this is a risk so, while the Yamato takes measures to minimize her sensor silhouette, Delta 5 modify the New Horizons long-range shuttle as a decoy able to fool sensors, at least in the nebula, that it is in fact a Constitution-class starship. The plan works and as the USS Yamato works its way through the Azure Nebula, limited sensor data through the interference shows that a pair of Klingon vessels have entered the nebula and appear to be following the false trail laid by the shuttle. When one of the Klingons gets close enough to possibly uncover the ruse, S'Chal is able to disable it by using the shuttle's phasers to detonate a cloud of volatile gasses. This also covers the shuttle from the second Klingon ship long enough to reach the other side of the nebula, hoping that they succeeded in distracting their pursuers enough for the Yamato to also make the traversal. Before the shuttle can contact the Yamato to verify they suddenly come under attack from an Orion scout ship. Despite being outgunned, Delta 5 are able to disable the Orions without taking any major damage. The second Klingon ship soon catches up with them, but Delta 5 receive reinforcements from the USS Yamato and the Starfleet vessels sent to meet her. Outmaneuvered, the Klingons stand down and return to their own space as the shuttle returns to the Yamato and the long-lost ship heads towards Starbase with her escort.
The USS Yamato has returned to the Alpha Quadrant, two years after having been believed lost with all hands. The return coincides with the end of the Yamato's 5-year mission, the first completed by the ves-sel after failures under several previous crews. Starfleet Command has arranged an event to celebrate not only the Yamato's safe return but also the many discoveries made by the ship and her crew. The event is held at Starbase One, and various Starfleet and Federation dignitaries are present as well as the senior officers from the Na-Zek. Surprisingly the Romulans have also accepted an invitation to join the celebration. Among the Romulan delegation are Commander Sheva and Centurions Pathauna and Vajan of the Sacred Blade.
During the celebration the members of Delta 5, as well as some of the Romulans and Na-Zek, receive a telepathic distress call from S'Chal, who was not at the celebration as he had been assigned to Starfleet Security for a classified mission. Delta 5 inform Capt. Sloane about the warning, and by questioning some of the senior Starfleet officers present she learns that S'Chal had been sent to the VC298 to check on a Federation Science Team on that world. Given the connection of VC298 to the extradimensional threat the Yamato fought in the Small Magellanic Cloud everyone familiar with that threat is concerned. With time of the essence, Commander Sheva offers some help. Also offering some surprise assistance is Ambassador Sarek of Vulcan, who had been made aware of the situation. While Capt. Sloane works through official channels, Delta 5 (along with USS Yamato Security Chief Na-Drade), the Na-Zek science and security officers, and Centurions Pathauna and Vajan all sneak away and use a rigged transporter to beam from Starbase One to a secretly cloaked Bird of Prey scout that had accompanied the Romulan delegation. Pathauna takes command of the Bird of Prey and sets course for the VC298 system.
Reaching the VC298 system the group sees no sign of any other starships, but residual readings indicate that the planetary defense system on the fourth planet, the same that had tossed the USS Yamato sever-al light years, may have recently fired. The scout ship approaches the planet under cloak and Delta 5, Lt. Cmdr. Na-Drade, and the two Na-Zk,l are beamed down to the ancient ruins on the planet. They find evi-dence that the Science Team had become corrupted by the extradimensional Outsiders. They travel to the underground city Delta 5 had found on their first mission here and come under attack by corrupted Starfleet Security forces. Stunning the Security officers, the group proceeds into the city where they are able to detect S'Chal's Aenar life signs since they are unique to any others in the city.
Deelo, Lt. Cmdr. Na-Drade, and Na-Zek Security Officer Grimma are able to save S'Chal from becoming a sacrifice and he tells the group how he came to that predicament. He was pulled from the Yamato to join a Starfleet Security team investigating the archaeological efforts on VC298 IV, but upon arriving on the planet the team was ambushed by the archaeologists and overwhelmed by the surprising aggressive-ness of the scientists and their numbers. S'Chal and the others who survived the ambush were taken down the underground city, with S'Chal sending the desperate telepathic warning before he was forced to turn all his willpower towards withstanding the psychic onslaught. Having been separated from the rest of the security team, S'Chal was unable to prevent them from becoming corrupted. Once his captors real-ized he could not be broken, S'Chal was tortured and prepared to be sacrificed, though to exactly what he does not know.
Though weakened by his ordeal, S'Chal rejoins Delta 5, Lt. Cmdr. Na-Drade and the two Na-Zek as they make their way to the massive Control Tower at the center of the underground city. Evading other cor-rupted Starfleet Security, the group enters tunnels beneath the Control Tower and find the Federation Scientists have been attempting to free an Outsider that had been entrapped millions of years earlier by the beings former slaves who had revolted and overthrown their oppressors. The being was held in a four-dimensional prison but is now almost free, though still mostly out of phase. Still, it is able to psychi-cally attack, and its corrupted followers attack the new arrivals with great fervor. Deelo, Drake and Vasquez, aided by Armitage, work on how to restore the prison while the others deal with the corrupted servants of the Outsider. While it is close, the group succeeds in defeating the corrupted Starfleet per-sonnel and restoring the dimensional prison, once again sealing the Outsider away from the material universe.
Once they leave the city, the group discover that the Romulan scout ship has been joined by Capt. Sloane aboard the USS Yamato. Delta 5 are beamed back aboard, as are the corrupted security team and scientists, who are held in Sick Bay with the hope that they can be cured. The Romulans return to their space, with the thanks of Capt. Sloane for the assistance, and the USS Yamato returns triumphantly to Starfleet Headquarters, truly putting an end to its 5-year mission. While Capt. Sloane and several of her senior officers have selected to remain at Headquarters to help oversee the USS Yamato's almost two years long refit to Constitution II class, the members of Delta 5 receive promotions and prepare to head off to their new assignments.
The Class-M planet Delphi Taurus IV at first glance appears to be an ideal location for potential colonization. Earth-like conditions, ample vegetation and small-scale animal life; but the planet has a secret. The planet is a singular organism, not sentient but all life on the world (both plant and animal) are connected through a single psychic nervous system.
VC298 is an F-type (yellow-white) star with six planets, unusual in that none of them are gas giants. VC298 IV is a Class M planet with two small airless moons; VC298 I is a Class D airless rock, VC298 II is a Class H desert world with a thin unbreathable atmosphere, VC298 III is a Class Y world with a highly corrosive atmosphere, VC298 V is another airless rock and at the far end of the system is VC298 VI which is a Class K ice world with a marginal atmosphere. VC298 IV contains the ruins of an ancient civilization that included a powerful planetary defense system that attacked the Yamato, causing a landing party to be temporarily abandoned on the surface.
Styx is the name given to an unusual stellar phenomenon known as a dark nebula. The nebula has a spinning neutron star at its center, designated Styx I, which is also unusual in that it is the only known instance of an irregular pulsar. The nebula has another surprise, Styx I has a planet orbiting it. The planet has a highly elliptical orbit as well as a highly eccentric one, circling the star at 30° above the plane of the system.
The Shackleton Expanse is a large, unexplored region of undetermined size that lies several hundred light years from Federation space, in a part of the Beta Quadrant that also touches on the far borders of Romulan and Klingon space. Based on Federation records, the handful of unmanned deep space probes so far sent to the Expanse all stopped transmitting data shortly after entering the region, leaving it a vast mystery just off the edge of the map. What little is known about the Expanse comes from the small amounts of data the long-range sensor probes had collected and the stories and legends that have been culled from independent traders who claimed to travel in and near the Expanse. Surveys and personal logs from these traders are rife with unsubstantiated reports of subspace interference, electromagnetic waveforms, tetryonic storms, and more, in addition to a litany of anecdotes that veer far from the factual and well into the fanciful with stories of "whispers in the Expanse" and "ghost ships". The USS Yamato found herself in the Shackleton Expanse after traversing a wormhole from the far side of the Beta Quadrant.
The USS Yamato had to traverse the Triangle in order to safely return to Federation space. See the detailed breakdown on the Triangle Sector.
The Class-M planet Delphi Taurus IV at first glance appears to be an ideal location for potential colonization. Earth-like conditions, ample vegetation and small-scale animal life; but the planet has a secret. The planet is a singular organism, not sentient but all life on the world (both plant and animal) are connected through a single psychic nervous system.
The Aerolith are beings of pure energy who have inhabited the Milky Way Galaxy for millions of years. All that is known of them is based on what they chose to reveal in their encounter with Delta 5, including their claim that they were part of an alliance of races that drove a hostile force from the galaxy millions of years ago. The Aerolith may have once had corporeal forms but evolved beyond them much like the Organians.
The Scorpion Horde are a migratory predatory arachnid species possibly native to the Small Magellanic Cloud, though this is not known for sure as they have the ability to travel interstellar distances in a form of hibernation so could originate from outside the dwarf galaxy. The Horde is hive-based, with a hierarchy of castes. Much of this is assumed, but given the swarm behavior it is extremely likely there is at minimum a leader caste like a Queen. The Soldiers are typically the only ones encountered by other races, but evidence points to a dedicated cast being responsible for generating the resin tendrils used to attack ships as the resin production capabilities observed in Soldiers are insufficient to create the tendrils. The resin that the Horde uses to form their hives and trap prey is a polarized silicon-based material that has high strength and is impermeable to most forms of electromagnetic radiation. This includes blocking sensor scans, making it impossible to get readings of the interior of the hive. Most Horde castes have a carapace that has simi-lar properties. The resin is typically a dark amber color and a typically smooth surface. While it is initially liquid when extruded the resin hardens quickly.
The Yamato is being sent to Theta Leoonis to make first contact with a species called the Atyansa. The initial survey describes the species as highly intelligent and peaceful. The survey team called the Atyansa "uniquely prepared for contact"; apparently despite having a technological level roughly equivalent to 16th Century Earth they Atyansa were not only aware of interstellar travel and the existence of alien species, they were also aware of the Federation and specifically requested the USS Yamato by name.
The Gith are a race of six-limbed cephalopods, similar to an Earth octopus. Their head/body averages one meter in length, with their tentacles being of roughly equal length. They lack suckers and instead have a series of articulated manipulators running along each limb, each anatomically similar to insect limbs. They have two eyes (perceiving wavelengths towards the infrared end of the spectrum) that are on short articulated stalks that gives them a wide angle of vision. The cranial bulge has a hardened carapace similar to a nautilus shell protecting it. Like octopi they have no skeletons. They appear to eat through a circular mouth on their underside that contains rings of serrated teeth; the orifice also serving as an excretory organ. They seem to mostly and they can channel jets of water through it to propel them along.
The Wanderers are religious pilgrims traveling in spacecraft in pursuit of the Omen, an astronomical phenomenon known to several worlds in this region of space. The Wanderers remember when the Omen passed over their original world and caused the end to a devastating war. Once the people of that world achieved interstellar flight the Wanderer pilgrims set off in search of the Omen. They have found several other worlds that have also been impacted by the Omen, and picked up new followers along the way.
The Intergalactic Alliance is the name used by the loose coalition of ships that have found themselves pulled into the Small Magellanic Cloud by the fractured transport network that once connected the Milky Way Galaxy and its satellite Dwarf Galaxies and Globular Clusters. The Alliance is made of six different alien races: