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.
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 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: