Prelude
Captain James Winters and his First Officer, Commander Kevin Johnson, are on Luna awaiting the completion of the Constitution Class heavy cruiser USS Yamato when an explosion sets off a devastating Moon-quake. Hundreds are killed, including Captain Winters. The explosion was the result of a terrorist attack and responsibility is claimed by insurgents from Altair III. They warn that more attacks will occur if the Federation continues to interfere in the Altairian conflict. Intelligence reports say that the insurgents could not be from Altair III, but the public outcry over the Luna attack may force the Federation to send in Starfleet to end the conflict.
Commander Johnson is promoted to Captain and given command of the Yamato.
Part 1 - Stardate 1046.5
The Yamato arrives at the Altair system and an undercover landing party goes to Altair VI in an attempt to discover who is supplying that world with advanced weaponry. The team is nearly captured but they escape with the assistance of an underground anti-government movement who are seeking an end to the war.
Part 2 - Stardate 1048.9
The landing party discovers that the advanced weapons are smuggled in as medical supplies. They return to the Yamato and intercept the next shipment. The weapons are being supplied by Orion pirates. The revelation that their government was conspiring with off-worlders allows the rebel movement to overthrow the current regime. The war is ended and negotiations between Altair VI and Altair III begin to form a single system-wide government
Stardate 1193.4
While exploring the Epsilon Hydrax system the Yamato discovers a recorder buoy from the SS Hercules, a DY-500-C class ship, lost over 170 years earlier. Investigating a nearby Class M world they discover that the descendants of survivors from the Hercules have set themselves up as rulers of a medieval society. The rulers are beamed up to the Yamato where it is revealed that these three are not descendants of survivors but are three of the original crew members. They've been infected by an alien virus akin to vampirism and they use their powers to take over the ship. Dr. Chang captures them using the transporter and gives infected crew members, including Captain Johnson and Lt. Malone, a complete blood transfusion to rid their systems of the virus. The vampires are sent to a Vulcan manned research station where they can be examined safely as Vulcans are immune to the vampire's mind powers and the vampires cannot consume Vulcan blood.
Stardate 1247.5
The Yamato is on patrol in Gamma Hydra Section 13 when war erupts between the Federation and the Klingon Empire. The Yamato defends itself successfully against an attack by three Klingon warships but it is damaged. After completing as many repairs as possible, the Yamato heads for Organia only to be stopped when the Organians impose a peace treaty on both powers to stop the war.
Stardate 1371.6
Investigating the loss of contact with the colony on Ariel IV, the crew of the Yamato find the planet, a desert world, overgrown with vegetation. The landing party can find no trace of the colony and they discover that the vegetation is not native to Ariel IV. Meanwhile, in orbit, the Yamato passes through a strange cloud. Repairing damage to the ship's hull, an engineer is infected by some kind of spore. Feeling ill, he goes to sick bay and, in front of a horrified Dr. Chang, turns into a tree and tries to take root in sick bay. Discovering that the spores came from the mysterious cloud, the Yamato destroys the cloud then follows the trail back to its planet of origin. The spores were the result of an attempt to create an aggressive plant species that could survive on the ecologically devastated world. The plants were too aggressive and overran the whole planet. Spores given off from the plants would leave orbit and drift through space until they found another world where they could grow. The Yamato uses its phasers to destroy the biosphere of the planet, ensuring that no more of the menacing spores are produced.
Stardate 1523.6
When beaming down to the surface of Dryad V, a malfunction disables the transporter stranding the landing party and rendering them unconscious. When the group awakens they have been captured by natives, all except Lt. Malone who is nowhere to be seen. Their captors destroy the communicators when the ship tries to contact the landing party. While attempting to overpower their guards a security officer is killed, so the rest of the group bolt for nearby wilderness. They evade their pursuers by going into the desert seeking shelter in a group of nearby mountains.
Meanwhile, Lt. Malone discovers a band of rebels who oppose the Church of the Triumvirate, who appear to be tyrants in control of the whole planet. Also, the rebels seem to regard Malone as some kind of savior and worship him almost as a god.
In the mountains, the rest of the landing party find a hermit who knows about the Federation and has a phaser. Together with the hermit the remaining landing party members (Lt. Cmdr. Andropopoliv, Dr. Chang, and Science Officer Massad) go to the rebel encampment where it is discovered that the hermit is Joseph Malone, the older brother of the Yamato's Lt. Malone. The elder Malone had been a lieutenant on the USS Gulliver, which had been destroyed presumably with all hands lost. Malone had been in command of a landing party aboard a shuttlecraft and they had crashed on Dryad V. The Church killed all of the party except Malone and used the group's phasers to take over the planet. Malone escaped and joined the rebellion. He used his phaser to set up an overload in the phasers that the Church had taken. The resulting explosion killed not only members of the Church's army but wiped out a group of nearby rebels as well. Overcome with guilt, Malone exiled himself to the desert.
The happy family reunion is spoiled when it is learned that the Army, using the Yamato landing party's captured phasers, is approaching the rebel camp. The younger Lt. Malone remains with the rebels while the others, along with the elder Malone, sneak into the capital to recover the communications gear from the Gulliver shuttle. The party contacts the Yamato and beams aboard, along with all remaining equipment from the shuttle, and the ship uses its phasers to stun both the army and the rebels. They take back the stolen phasers and beam the unconscious rebels to safety. With all of the stolen technology back in Federation hands, the Yamato leaves orbit heading for the nearest star base to drop off Joseph Malone.
Stardate 1754.5
Investigating the planet Alpha Z-21, supposedly home to an advanced race, the Yamato discovers that the planet is being overrun by machines. They find the last of the population crowded into a cluster of small villages. It seems that the central computer which controlled construction (every aspect of life was automated, leaving the populace with nothing but spare time) malfunctioned and began building new cities. The people did not know how to defend themselves since their every need had been provided for. When raw materials ran out, the computer invented a synthetic metal. Disaster truly struck when the automated food producers broke down. No one knew how to repair them and, since they had no agricultural skills, the remaining populace would soon starve; if the city builders did not build over what little open land remained first. The synthetic metal proved resistant to phasers but Chief Engineer Solek and Dr. Chang discover that it does possess a weakness; simple nitric acid breaks down the metal. The Alphans and the crew of the Yamato are quickly able to destroy the city builders and disable the central computer. Captain Johnson promises the people Federation assistance in rebuilding their society.
Stardate 1908.1
The Yamato comes across of the scout ship USS Carson, which has been missing for several weeks. The ship's power has been drained and there is no sign of the crew. Long range sensors detect a Klingon cruiser and the Yamato begins pursuit. Both ships are caught in a powerful tractor beam around a planet and the ship's power is slowly being drained. Suddenly, the command crew is beamed away from the bridge by a strange transporter beam and they find themselves in what appears to be 1890s London. It's turns out that the whole planet is divided into regions, each one representing a different genre based on Earth literature. Other regions they discover include King Arthur's Camelot, Sherwood Forest and Robin Hood, Shakespeare's Henry V at Agincourt, and Ian Fleming's James Bond. Accompanied by inhabitants from different regions, the Yamato's command crew capture a group of Klingons, also trapped here, and find survivors from the Carson's crew who had similarly been transported to the planet. They also find the central control which has been taken over by the "villains" from the different regions, who have been attempting to take over the planet. The group destroys the central control and this frees both the Yamato and the Klingon ship. The Klingons return to their territory and the planet is discovered to be similar to the Shore Leave world encountered by the USS Enterprise, but this one malfunctioned and tapped into the Federation's Memory Alpha archives to create the patchwork world. With the central computer destroyed, no new regions are created but the existing regions remain.
Stardate 2090.7
Chief Engineer Solek, Dr. Chang, and Lt. Malone along with Federation Ambassador Carlos Rivera, are en route to the Lorealyn system when they are captured by a Klingon battle cruiser. Both the Federation and the Klingons want Lorealyn IV and Rivera was to be the UFP representative at the negotiations. The Klingons desperately want the world for its strategic value but cannot take it by force because of the Organians, so they must use different tactics. The three officers escape from their cells and rescue the ambassador. They escape from the cruiser via shuttle and reach the Yamato safely. When the Lorealyn people learn of this Klingon treachery they choose to join the Federation.
Stardate 2251.6
When the Yamato ferries VIPs to the independence ceremonies on the planet Kintara, a former earth colony that has chosen to withdraw from the Federation, the command crew attend a dinner party hosted by Representative Terrelion Pang. At the party, a woman named Marna Grard collapses after claiming to have seen the ghost of her dead husband. At the hospital, Marna slips into a coma and dies. Dr. Chang finds the circumstances of her death suspicious and wonders about the physician who was treating her, Dr. Sendat.
The group spends the night at the house of Olberan, a famous explorer who was at the party as well. In the morning they find that Hortan Velid, president of the newly independent world, has banned the mysterious mineral starjade for supposedly possessing harmful properties, has forbidden access to the unexplored northern continent (where starjade is found), and has arrested several individuals for allegedly covering up the information that starjade is dangerous. One of those arrested is Senator Pang. Furious, Olberan wants to go to the capital to confront President Velid, but before he can leave the host is attacked by members of the Star Guard, Velid's private army and now the law enforcement of Kintara. Solek is captured but the others escape.
Realizing that it would be dangerous to keep the political prisoners in a conventional jail, the group believe that Solek and Senator Pang are being held at the President's villa. Sneaking into the villa they discover an underground lab and see Dr. Sendat using some kind of black orb to drain Solek's life force, apparently killing him. Much to Sendat's shock, Solek is alive and in the confusion Solek and Senator Pang escape with the rest of the group.
Guided by Olberan's pet Cheeber, a type of monkey-like animal that are from the northern continent and as it turns out are also semi-telepathic, the group heads to the northern continent and finds a camp patrolled by Star Guard forces and using Cheebers as slave workers. The camp is built around a crashed alien spacecraft. Inside the craft, the group discovers a control room with a larger version of the black orb that Sendat used. Just then, Velid himself arrives with a contingent of Star Guards. Olberan turns out to be working for Velid and the team is captured. Velid explains that the orb drains life force and he can then use this life force to increase the strength and endurance of his troops. Velid tells Solek to touch the orb; Velid wants to add to the strength of the Vulcan to his men. Malone tops Olberan from warning Velid that Solek is immune and Velid cannot believe it when the Vulcan simply picks up the orb and begins examining it. Velid grabs the orb and is killed instantly; the orb falling to the ground and shattering into a million pieces. The Star Guard suddenly lose their superhuman strength and are quickly overrun by hordes of Cheebers from the jungle.
Solek explains that the orb housed the last member of the alien crew, beings of pure psionic energy. When the orb was touched the alien would try to make contact but humans could not handle the psionic power and were killed. When Solek first touched the orb he managed to make telepathic contact with the alien and knew that it wanted to be free. By destroying the orb, the alien was released. The reason for the ghost sightings was that the Cheebers who were working around the craft would pick up psionic residue from the orb's victims and, due to starjade which boosts telepathic signals, would transmit those images to Cheebers on the south continent who were pets. When one of those Cheebers was near someone with strong emotional ties to someone killed by the orb, the Cheeber would unintentionally transmit the images to that person, especially if there was starjade nearby (which was often since it was used in making jewelry).
Senator Pang takes over the government of Kintara until Velid's corrupt establishment is removed and new elections held, though Pang believes that the Kintaran people will probably choose to rejoin the Federation.
Stardate 2311.4
The Yamato is taken over by an alien calling himself Nomad. He says that he needs the ship to return to his home. He takes the Yamato through a space warp to his planet and invites the crew to visit the world, which he describes as a utopia. Beaming down to the surface nomad finds that his brother, who built the robot servants of this world, has used the robots to seize power and now rules with an iron fist. Nomad and the Yamato's command crew are captured but they escape along with hundreds of other prisoners. They overrun the brother's robot guards and Nomad destroys his brother's gigantic mechanoid, which doubled as his throne and housed the controls are the robots. His people free, Nomad thanks the Yamato crew and sends the ship back to Federation space.
Stardate 2493.5
In an unexplored region of space, the Yamato race against the Romulans for the treasures of an ancient race. The crew must confront the Romulans on the lost world of the ancients, hidden deep within a nova shell.
Stardate 2613.2
The crew is overcome by a strange disease and rogue Klingons capture the ship, intent on bringing it to the Empire and regaining their lost honor. The crew's only hope lies in a group of stowaways - a family of Cheebers that has been hiding aboard since the Yamato's visit to Kintara.
Stardate 2684.9
A shuttlecraft crashes on a primitive world and the passengers must repair the radio and contact the Yamato before it must leave on a vital mission, abandoning the search for the shuttle. The planet is inhabited and its society is in the midst of a Dark Ages religious inquisition. The dilithium crystals that are needed for the repairs are considered sacred stones by the populace and are believed to have mysterious powers, so the survivors of the crash must complete the repairs without violating the Prime Directive.
Stardate 2851.6
A Doomsday Machine is headed for the neutral world of Ectair. The Yamato reluctantly joins forces with the Romulan vessel Raptor in order to save the planet. Despite treachery on the part of the Romulans, the crew of the Yamato are able to defeat the Doomsday Machine and save the people of Ectair.
Stardate 2990.2
The Federation is negotiating with the people of Jehan, the planet in the Organian treaty zone. The Jehahes abandoned much of their technology millennia ago and have developed their intellects to an incredible degree. They are religiously opposed to computers of all kinds. The crew of the Yamato and the Federation representatives are caught in a war between factions, one of which is secretly being backed by the Klingons.
Stardate 3115.1
The Yamato discovers a sleeper ship containing the last of the Corillian race in suspended animation. Reviving the crew of the sleeper ship, the Yamato leans that the Corillians had been a technologically advanced race with a small but prosperous empire. Over three hundred years ago the Corrillians encountered the expansionistic fledgling Romulan Star Empire. Though technologically outmatched by the Corrillians, the Romulans made up for this in sheer numbers and the Corrillians became the first race subjugated, and later slaughtered, by the Romulans. Now awakened, the last Corrillians seize control of the Yamato intent on taking vengeance on those who slaughtered their people. The crew of the Yamato must regain control before the Corrillians start a war between the Federation and the Romulans.
Stardate 3219.3
Assigned to shut down a Federation Research Station on the planet Aleph III, the Yamato comes into conflict with a Klingon vessel sent to steal valuable scientific data from the station. Complicating matters are the presence of the Research Station's subjects roaming the surface of the barely habitable world - genetically modified creatures including what appears to be a surprisingly hostile breed of the normally docile tribbles.
Stardate 3363.5
While pursuing a Klingon warship the Yamato and her quarry become trapped in a "Bermuda Triangle of Space" where time does not pass and where many ancient space vessels have become similarly trapped over the millennia. The crew of the Yamato save the other crews trapped in the region from the aggressive Klingons, then must team up with the Klingons to escape. The crews of the ancient vessels, having long ago learned to live together in peace in this strange realm decline an offer to escape with the two ships.
Stardate 3425.7
The Yamato is assigned to recover the logs and science data from the USS Hood, which has become trapped in a spatial anomaly while examining a rare double neutron star system. The Hood has become trapped in an interphase space, which had driven the crew insane causing them to turn on each other in a murderous rage. The Yamato's landing party recover the data, and seek a means to rescue the surviving crew of the Hood before the ship is lost forever in another dimension.
Stardate Unknown
While searching for the missing USS Republic, the Yamato herself is lost.