- A.D 2202 - Revive, Space Battleship Yamato: The Gatlantean warlord Zordar vows to bring "love" to the universe through a campaign of death. His troops attack the planet Telezart and kill its ministers. Near a Gamilas base, Earth and Gamilas forces work together to oust a fleet of Gatlantis warships from a Gamilas territory. When a Gatlantis heavy destroyer appears, the coalition fleet appears to be overpowered. However, the UNCF (United Nations Cosmo Force) battleship Andromeda attacks with its powerful Wave Motion Gun, destroying the bulk of the Gatlantis forces. However, a Gatlantis heavy destroyer manages to warp its way to Earth, heading on a collision course with UNCF HQ. The Yamato, undergoing modifications, is quickly called into service, and destroys the Gatlantis capital ship with its main shock cannons. Meanwhile, Kodai receives a strange message from the ghost of Captain Okita, urging him to return to the Yamato.
- Tension - Reach the Embassy on the Moon: A fleet of advanced Andromeda-class warships are launched in a grand ceremony. The crew of the Yamato meet at Okita’s grave to honor his memory. Sanada, Kodai and Shima examine the Yamato’s auto-recording log, which reveals a call for help from a mysterious woman. A Gamilas spy named Keyman tells Kodai to seek answers on the moon, where the Gamilas Embassy is located. With an assist from Yamamoto, Kodai breaches the lunar defense grid incognito. Meanwhile, Zordar begins creating a planetary blockade around Telezart and then seta Gatlantis on a course for Earth, the target of Teresa’s transmission.
- Shock - Legacy of the Cosmo Reverse: On the moon, a Gamilas ambassador informs Kodai about Gatlantis and its desire to take power from Teresa, the goddess of Telezart. Soon back on Earth, Keyman shows Kodai the Cosmo Reverse Time Fault, a secret cave in which 10 days pass for each outside day. This Iscandarian technology has given Earth time to build a fleet of ships like the Andromeda in a very short time. When Kodai asks the UNCF to approve a rescue mission to Telezart, they turn him down and try to reassign the Yamato crew members. Kodai gathers the crew and urges them to leave with him on the Yamato anyways. On the 11th planet of the Solar System, a Gamilas outpost is attacked by advance Gatlantis forces.
- Departure to the Unknown!: Earth HQ attempts to dissuade the Yamato from taking off, but Kodai and the crew are undeterred from their decision answer Teresa's call for help. The Yamato fights its way out of its underwater dock and takes to the sky. In the Earth's atmosphere, a defense satellite is armed. The Yamato destroys it and heads out into deep space.
- Clash! Yamato vs. Andromeda: The Cosmo Tigers, led by Yamamoto, join the Yamato near the moon. The Gamilas Keyman also arrives, insisting on being an advisor to the Yamato's crew. Soon, the Andromeda, led by Captain Yamanami, moves to intercept the Yamato near Jupiter. The Yamato uses the asteroid belt to form a ring defense, and eventually manages to push past the Andromeda. Moments later, their mission is approved by the UNCF due to political pressure from the Gamilas. Kato and the remaining fighter pilots also soon arrive at the ship.
- Battle to the Death - The 11th Planet Rescue Operation: Comet Empire forces under General Nazca continue to attack the Gamilas colony on the 11th planet, which is defended by a small force of Cosmo Cavalry stationed there. When the Yamato learns of this attack from a survivor, they decide to warp in close to the surface, although this will temporarily take the Wave Motion Engine offline. This done, the survivors board the Yamato, but the vulnerable Yamato is pinned down by Nazca’s heavy destroyers. Soon more Gatlantis battleships arrive and a massive energy beam is fired at the planet, apparently destroying the Yamato.
- The Beam of Light Flashes! The Radiance of the Wave Motion Gun: The Yamato uses its Wave Motion shields to hold a mountain of rocks at bay. It later uses the ring defense mechanism to further control the rocks while repairs are underway on the ship. A massive Gatlantis fleet under General Mazer amasses near the artificial sun orbiting the 11th planet, intending to draw on the sun’s power to fire a devastating beam at Earth (the Legionnaire Cannon). Although uncomfortable with breaking Okita’s promise to Starsha, Kodai allows the Wave Motion Gun to be fired. He allows this because the blast does not cause any enemy casualties - it only hits the sun, causing a resonance wave which disables Mazer’s Gatlantis fleet without destroying them. Mazer is confused and furious by Kodai’s act of mercy.
- Trap at Planet Stravaze!: The Yamato arrives at Stravaze, a planet where they plan to drop off the 11th planet refugees with a Gamilas force on its way to Earth. However, while on the surface, a suspicious-looking woman named Katsuragi leads Kodai to a cave of crystalline obelisks, where he is confronted by a "zombie" possessed by the consciousness of Zordar. At the same time, a rebel Gamilas force (the Destructive Liberation Army) attacks Stravaze, lured there by Keyman allies. Keyman uses this distraction to take the opportunity to implant a secret element in the Wave Motion Engine.
- Zordar, The Devil's Alternative: With Kodai on the planet’s surface, Admiral Hijikata takes command of the Yamato and draws the enemy DLA fleet away from the Gamilas refugee ships. In the Aquarius cave, Zordar tells Kodai that Gatlanteans are manufactured warriors, and that he wants to destroy all lifeforms who possess emotion (due to their unstable, self-destructive nature). He also informs Kodai that he has placed one of his zombies on each of the three Gamilas refugee ships. Kodai must choose one of the ships to be spared or Zordar will order all three puppets to self-destruct. More importantly, with Yuki serving as an escort aboard one of the three ships, Zordar tries to force Kodai to choose Yuki’s ship to be saved over the lives of the other two. When Yuki learns of this terrible dilemma that Kodai faces, she jumps overboard in order to spare Kodai from having to make such an unwinnable choice. Kodai takes a desperate plunge in his shuttle in an attempt to catch Yuki in mid-air. Angry that his plot to torture Kodai has failed, Zordar orders his zombies to self-destruct and the three damaged refugee ships also begin falling towards Stravaze's surface. In a wild move, Hijikata has the Yamato destroy the gravitational core of Stravaze with the Wave Motion Gun, leaving Kodai, Yuki and the refugee ships all drifting weightlessly in space.
- Spellbound: The Space Fireflies Beckon a Crisis: The Yamato encounters “space fireflies” (starflies) which mesmerize the crew (and heighten emotions to the extent of nearly causing a fight between Kodai and Saito). Even worse, they cause deterioration to the ship itself. Keyman helps Sanada deactivate the mesmerizing effect of the starflies with a frequency burst, while Dr. Sado uses a chemical spray to kill off the starflies themselves. The crew then receive a vision from Teresa, further encouraging them on their journey to Telezart. On Gatlantis, Zordar gifts Desslar with a Gatlantean fleet to command.
- Desslar's Challenge!: Desslar uses his newly-improved Desslar Cannon to destroy the remnants of General Mazer’s “contaminated fleet”, as per Zordar’s orders. He then tracks down the Yamato with the help of his Gatlantean aide Miru (who psychically receives Yamato's coordinates from Katsuragi). Using warp torpedoes, Desslar lures the Yamato into a high energy zone where they cannot use the Wave Motion Engine without causing an explosion. The Yamato soon encounter an Aquarian tube-shaped relic, which they enter and investigate. Desslar’s forces arrive in the high energy area and the Desslar Cannon is fired at the Aquarian tunnel relic. The shockwave propels the Yamato with enough force to allow it to go into warp and escape. Desslar then reunites with a fleet of Gamilas loyalists, who suddenly warp in, surprising Miru. On the Yamato, Keyman recognizes the Desslar Cannon’s energy signature.
- The Shocking White Comet Empire: The Yamato Rams Through!: Katsuragi is exposed as a Gatlantis spy and goes into hiding on the Yamato. The White Comet suddenly appears in front of the Yamato. In Gatlantis, Sabera uses her organ-playing power to use gravitational waves on the Yamato, drawing it towards the core of the White Comet. Being identical manifestations of the same being in the same time-space, Sabera and Katsuragi begin to “resonate” with each other. An angered Zordar kills the out-of-control Sabera, who begins to experience “forbidden emotions”. This allows the Yamato to warp out of danger and continue towards Telezart.
- The Telezart Landing Operation: Strike the Enemy Missile Fleet!: Gatlantis General Gorland and his clone heir guard the approach to Telezart. The Yamato and an armored mobile suit brigade warp in behind Gorland’s forces and attack from the Telezart side. Gorland fires an anti-matter missile at a rock formation situated in between the opposing forces, causing massive turbulence and throwing the Yamato’s original plan awry. Despite Okita’s promise to Starsha, Kodai is forced to use the Wave Motion Gun to obliterate Gorland’s forces.
- The Zavaival Onslaught: Finding Teresa: While Sanada and Kodai prepare Wave Motion Excavation Warheads to remove the planetary shell placed around Telezart by Zordar, Saito and Yamamoto lead their armored mobile suit brigade onto the surface in order to deal with Gatlantis General Zavaival’s robot tank corp. Zavaival employs a Gamilas Reflex Gun against Kodai and Sanada but Keyman's knowledge of Gamilas tech allows him to sabotage it. After Zavaival and his forces are destroyed, Kodai, Sanada and Saito visit a cavernous sanctuary on Telezart where they finally meet Teresa. Teresa tells them that Zordar is using an Aquarian failsafe weapon with the intention of destroying all life in the universe. Suddenly, Desslar appears behind the Yamato crew members.
- Teresa, Cry for Desslar!: Teresa reveals that Desslar’s despotic actions in the past had only been for the benefit of his home planet. The people of Gamilas need a new planet to migrate to, since Gamilas will soon become uninhabitable. Keyman arrives and reveals himself to be Desslar’s nephew, whose mother Desslar had exiled many years ago from the royalty. Above the planet, Desslar’s fleet begins attacking the Yamato, driving the ship down to the surface of Telezart.
- So Long, Teresa! The Bouquet of Two Desslars: With the help of Keyman’s earlier sabotage of the Wave Motion Engine, Desslar and his forces capture Kodai and the Yamato. Desslar intends to use Teresa as a bargaining chip with Zordar, hoping that Gatlantis will help him find a new planet to replace Gamilas. After Keyman learns the identity of the mastermind behind the Desslar loyalists on Gamilas (his true mission objective all along), he turns on Desslar and frees the Yamato. Teresa and Telezart both soon vanish from the universe.
- Saturn's Offshore Battle: Gather the Wave Motion Fleet!: Sanada suggests using Keyman’s Wave Motion Engine alteration to increase the power of Yamato’s Wave Motion Gun for a one-time super-shot (as a “Transit Wave Motion Gun”). UNCF forces engage Gatlantis General Balsey’s fleet at Saturn. Balsey attacks the forward fleet with giant ramming missiles (sword-shaped “Eaters”), but Admiral Yamanami’s fleet of Andromeda class warships warp in and the tide turns. Zordar clones a new Sabera, this one without emotions. Through Miru, he tells Desslar that Gatlantis will help him take back Gamilas if Desslar destroys the Yamato. He also mentally gives Katsuragi new instructions to turn Kato against the Yamato.
- Yamato's Despair: Once More, the Devil's Alternative: Yamanami’s fleet gains the upper hand when additional UNCF ships ambush Balsey’s forces from a hiding place beneath Saturn’s rings. This prompts Zordar to warp in to the Saturn battlezone. When the UNCF's Wave Motion Guns fire on the White Comet, the true nature of Gatlantis is revealed as a massive planet-sized structure enclosing several planets. Zordar initiates a gravity whirlpool which begins sucking in the UNCF fleet, destroying most of the ships (although Yamanami manages to escape). The Yamato arrives and attempts to use its enhanced Transit Wave Motion Gun, but Kato (the life of his son held ransom by Katsuragi) reactivates Keyman’s sabotage element, rendering the Wave Motion Engine (and Gun) powerless.
- Yamato's Successor, Its Name is Ginga: Most of the crew of the Yamato are evacuated to the Ginga, a new “Yamato-class” battleship which is powered by the Cosmo-Reverse System. Although without offensive armaments, the Ginga can deploy a Wave Motion Shield around an entire fleet, protecting it from Gatlantis fire. The Ginga is also enhanced with an AI system, and its captain (Saki Todo) explains that they need to hold Gatlantis back for 100 days during which time Earth can manufacture more ships in the Time Fault. Kato leads a dangerous mission to deploy Wave Motion bomb-drones amidst he Gatlantis fleet, which are soon detonated by a resonance frequency from the Ginga. The Yamato crash lands on one of the planets within the Gatlantis structure. Yuki loses her memory from the last 4 years.
- Gatlantis, the Cursed Child: The crew of the Yamato discover that they have landed on Zemulia, the original planet whose inhabitants had created the synthezoid slave Gatlanteans. A recorded AI explains that an advanced model of Gatlantean named Zordar had fallen in love with a Zemulian woman (Sabera), and for this crime the Zemulians had ended up executing Sabera (and Zordar’s child-clone). Seeking vengeance, Zordar had activated the Ark of Destruction (the Aquarian doomsday failsafe) and destroyed the Zemulians. Katsuragi is a clone of Sabera, the last Zemulian. In the meantime, the White Comet warps to Mars.
- Escape the Nightmare!!: Keyman learns that the Zemulians have created a failsafe device in case the Gatlanteans became dangerous - a device called a Golem. Unfortunately, Zordar is in possession of it. The Ginga is ordered to retreat from the battlefield so that it can function as a space ark for the remnants of humanity (the G-Plan). Yamanami leads an unmanned fleet of Andromeda-class ships in a last-ditch attempt to stop Gatlantis at Mars. At the same time, the Yamato moves to escape from Zemulia just as Zordar has the planet destroyed. Seeing the Yamato in trouble, Yamanami dashes forward in the Andromeda in a veritable suicide attack. Saki abandons the G-Plan and goes after Yamanami’s Andromeda, and then uses the Ginga’s Cosmo Reverse Wave Motion Lens to magnify the Andromeda’s Wave Motion Gun, giving it the firepower to destroy the Gatlantis gravity core powering Zordar’s Ark of Destruction. This saves the Yamato and temporarily disables Gatlantis' warp capability.
- The Destined Confrontation!: With Gatlantis momentarily halted at Mars, the Yamato is repaired at drydock. It soon heads back out but is intercepted by Desslar’s ship, the Neu Deusuler. Warned by Keyman, the Yamato does a short warp to avoid the Desslar Cannon, and rams the Neu Deusuler. Desslar uses androids to raid the Yamato but Keyman deactivates them with his knowledge of Gamilas technology. During the battle, Saito learns that he is a puppet of Zordar. When Keyman confronts Desslar on the Neu Deusuler’s bridge, Miru appears and tells Keyman that if he kills his uncle then Zordar will agree to spare Earth and Gamilas for 10,000 years.
- Warriors of Love: Just before Keyman shoots Desslar, Kodai appears and stops him. Miru (Zordar’s young clone) fires at Kodai but Yuki uses her body to take the bullet. Miru is impressed by this act of selfless love (even without her recent memory) and decides to make peace. Unfortunately, he is then killed by Desslar’s arriving guards. Saito undergoes radiation treatment in order to cut his ties with Zordar, although it shortens his lifespan. The White Comet arrives at Earth and tells humanity that it will spare Earth if they will become subjects of Gatlantis.
- Yamato, Attack the Comet Empire!: With protective assistance from Desslar’s capitol ship, the Yamato fires the Transit Wave Motion Gun at Gatlantis, breaching its main fleet, the first line of defense. Additional Gamilas ships (including Frakken’s subspace fleet) arrive and escort the Yamato into the heart of Gatlantis. Within the Ark of Destruction (Gatlantis’ main structure), Gatlantis cruisers are deployed against the Yamato. However, Katsuragi (now in opposition to Zordar’s ambitions) uses the Yamato’s remote cosmo-navigation system to take over control of Gatlantis’ unmanned defenses. When Zordar tries to take back control of his ships, Kodai uses the remaining Gatlantean forces still slaved to Katsuragi to mount a ring defense (a tactic used previously with asteroids). When Zordar telepathically discovers Katsuragi’s ship location he has her killed with a precise tactical strike. Tokugawa, Kato, Hijikata and Analyzer are also casualties in the general carnage. Finally, Kodai leads an away team to penetrate Zordar’s very throne room. When Zordar's father Gairen sacrifices his life to save his son, Zordar strikes his sword against his throne, which also happens to be the Golem failsafe device.
- Farewell, Space Battleship Yamato: The shattered Golem instantly kills all Gatlanteans everywhere in the universe except for Zordar (who is essentially an advanced form of Gatlantean, or “human”) and Sabera. Zordar then absorbs the Golem’s released energy to further evolve the Ark of Destruction into an even larger, bird-shaped form. Keyman and Saito sacrifice their lives when they detonate a Wave Motion Excavation bomb at the heart of the Ark, hoping to destroy the Ark's reaction chamber. Unfortunately, this is mostly in vain and Zordar uses the increased power of the Ark to destroy part of Earth’s moon. Kodai has everyone evacuate the Yamato and sets the Yamato on a collision course for Zordar’s Ark, hoping that his last act will buy Earth enough time to relaunch the Ginga and find a new planet for the remnants of mankind to live on. Yuki appears on the bridge and joins him in an embrace on the bridge. The Wave Motion Engine goes critical, causing a breach in space-time and allowing Teresa to manifest. Impressed by the will of humanity, Teresa accompanies the Yamato on their final journey, which climaxes in a flash of light (an explosion which destroys Zordar and his Ark of Destruction).
- Earth, Yamato Is ...: Six months after the end of the war with Gatlantis, the Yamato suddenly resurfaces in the Time Vault, carrying only one occupant, Yamamoto. Yamamoto explains that Kodai and Yuki are still living in Teresa’s higher dimension, thrust there during the destruction of Zordar's Ark. Sanada reasons that a rescue mission can be mounted to this higher dimension, but such a journey will completely deplete the Time Vault. A vote is put to the people of Earth, with Sanada arguing that the current path of infinite armament (through the power of the Time Vault) is not humanity’s true nature. Meanwhile in Teresa’s dimension, Kodai has reservations of returning to Earth, as he feels guilt for “pulling the trigger” on Gatlantis. He changes his mind when he learns that a baby will soon be in his and Yuki’s future. The Yamato soon arrives and everyone returns to Earth (and the Time Vault is destroyed).
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