- The Solar System Faces Destruction: A stray proton missile from battling Galman and Berth forces accidentally hits the Sun and causes an uncontrollable fusion reaction. Earth Command is told that the Earth will be uninhabitable in one year, so the Commander orders Kodai (now Captain) to take the Yamato and look for a "new" Earth to relocate to. Meanwhile, the Yamato is being refurbished in the Japanese mountains. New cadet Domon, whose parents were killed in the initial proton missile accident, joins the crew.
- Battle at the Milky Way: Earth's outposts at Alpha Centauri are attacked by the forces of the expanding Galman Empire led by General Dagon. Berth forces under Captain Ram intercept and attack them. The Yamato hurries to complete its preparations to launch, but is hindered by electromagnetic wave interference from the dying Sun.
- Yamato Departs at Dawn: As the Galman and Berth forces warp into Earth space, the Galmans almost discover the Yamato's launch base, but are intercepted by Yamato's fighters. Aihara meets a girl that he likes, and but says farewell to her as the Yamato takes off on its mission.
- Shoot Through Mars: On the Galman homeworld Desslar receives reports from his generals. The Yamato conducts warp and battle drills. More proton missiles enter the Solar System and the Yamato destroys them. New crewmember Domon is impressed by the crew's dedication.
- S.O.S Legendra: Near Neptune, the Yamato encounters and helps resupply the Berth ship, the Legendra. Dagon's Galman forces arrive and he decides to wait for Berth Captain Ram to finish resupplying. Dagon plans to destroy both the Legendra and the Yamato. When Ram nears planet Brumas, Dagon's battleships open fire on them and the Yamato. Kodai orders the Cosmo Tigers to attack.
- Battle Near Planet Brumas: Dagon's forces destroy the Berth ship Legendra. The Yamato does a fast vertical ascent to get distance from the Galman forces, then cuts power to make an emergency U-Turn. It then barrels through the Galman forces while spinning and firing. This maneuver forces Dagon to warp out and leave his other forces behind to cover for him. A Galman cruiser rams the Yamato and its soldiers begin boarding. The boarders are repelled and the Yamato escapes, but many young soldiers on both sides are killed.
- The Torment Seas of Alpha Centauri: The Yamato receives an SOS from Alpha Centauri so they land to investigate, as well as make repairs from the Brumas battle. Dagon finds the Yamato and sends missiles from his base on Barnard's Star. While Kodai and Shima are off the ship, the new crew prove their ability to bring down the missiles themselves. The Yamato takes off to investigate Barnard's Star.
- The Last Pioneer: Earth scientists attempts to cool the Sun with cooling energy beams, but fail. The Yamato lands at Barnard's Star and encounters Earth deserters. Meanwhile Galman General Dagon uses a new Reflex Gun (using ships instead of satellites) to attack the Yamato.
- Battle at Barnard's Star: Kodai uses the new Cosmo Hound fighter to locate the Refex Gun reflector ships and begins destroying them. Dagon sends out fighters and the Yamato responds by sending out the Cosmo Tigers. Kodai locates the Reflex Gun transmission centers and the Yamato destroys them with the main guns. Dagon fires a proton missile at the Yamato but Kodai uses the Wave Motion Gun to destroy it as well as the Galman base. Dagon however escapes. The Yamato leaves the Earthers as well as its female nurse division on an Earth transport.
- Dagon's New Fleet Strikes Back: Desslar gives Dagon reinforcements, not knowing that Dagon is fighting the Yamato and Earth. The Yamato aids a transport ship on the way to an observation station. Later the transport is destroyed by Dagon's forces, drawing the Yamato to Cygnus to investigate. The Cosmo Tigers intercept the Galman bombers, but the Galmans are faster to refuel and gain the upper hand. Shima attempts to warp, but a Galman torpedo disables the warp drive. The Yamato is forced to navigate towards the space tornadoes of Cygnus.
- Yamato in Danger at Cygnus: The Yamato heads for the space tornadoes but its engines are not functioning. Tokugawa's son uses Analyzer's body as a way to diagnose the problem. After escaping from the tornadoes, Dagon attacks using instant matter transporters. The Yamato's main guns are damaged from the tornadoes however, and the Cosmo Tigers are unable to launch after Dagon's fighters damage the hangar deck. The Yamato crew instead fight the attacking fighters with torpedoes and anti-aircraft artillery. Dagon orders his fighters to return and attacks with his carriers directly. The Yamato uses its now-repaired main guns and smokestack missiles to destroy the carriers. Dagon's flagship survives and warps, so the Yamato warps after it. When the Yamato arrives, Dagon puts the Yamato in a tractor beam and drags it towards a black hole. When Kodai fires the main guns at Dagon's ship, the gravitational forces deflect his shots. Kodai fires the Wave Motion Gun into the black hole and Dagon's ship is destroyed. General Gaidel, Dagon's superior, promises revenge.
- The Prison Planet: The Yamato lands on planet Berth, which is allied with the Bolar Federation and used as a prison camp. The prisoners pray to Mother Shalbart, who used to rule this region of space before the Bolar Federation came. The prisoners riot and then attempt to hijack the Yamato.
- The Deadly Bolar Federation: The Berth hijackers demand to be taken to planet Shalbart, but Kodai and the crew overpower them. On Galman, Desslar holds a meeting with his generals and when one of them reveals himself to be a follower of Mother Shalbart, he shoots him. Bolar commander Bemlayze arrives on Berth and orders the rebel prisoners to be executed. When Kodai objects, an argument erupts and Bemlayze tries to have the humans shot. The Cosmo Tigers save the Berth prisoners and the Yamato destroys the pursuing Bolar ships. However, Bemlayze has Berth destroyed by planet missiles and promises to meet the Yamato again.
- Subspace Submarine Captain Galman Wolf: General Gaidel enlists the Galman Wolf pack, Captain Frakken and his subspace submarines, to help him with the Yamato. The Galman Wolf pack warps to the Yamato's location and attacks while hidden in subspace, using torpedoes. Domon spots the periscopes of the Galman subs and the Yamato makes a warp to escape. Frakken warps in pursuit so Sanada begins creating a sonar device. The Yamato fires Wave Motion cartridges at one of the the submerged ships, forcing it to surface, at which point Kodai destroys it with the main guns. Frakken retaliates with more torpedoes and Kodai is injured when one strikes the bridge.
- Yamato Imprisoned: While Frakken regroups his forces, Dr. Sado sees to Kodai's wounds. Frakken sends one of his ships to the front of the Yamato and one to its rear as decoys. When Sanada's new subspace sonar detects them, Domon fires WM cartridges to make them surface and then destroys them with the main guns. However this gives Frakken's other ships time to position themselves and attack with torpedos from the right and left. Frakken sends the bulk of his force towards Gaidel's Eastern Command Space Fortress as a lure, and the Yamato follows them. Gaidel's mobile base, immune to blasts from the main guns, swallows the Yamato and imprisons it in a chamber lines with Reflex plates, preventing it from firing the Wave Motion Gun. When Desslar finds out that Gaidel has captured the Yamato he apologizes to Kodai and invites them to visit his new empire.
- Festive day for Desslar: Desslar explains to Kodai that the Galmans, the original ancestors of the Gamilons, had been under Bolar rule. Desslar liberated the Galmans and became their new leader, freeing the other planets in the area from the Bolar regime. Desslar invites Kodai and the crew to witness a parade of his military forces.
- Desslar's Empire in Crisis: Desslar promises to help Earth save the Sun. However Bolar missiles warp in and impact the Galman capital. A planet destroying missile approaches but Domon fires the Wave Motion Gun and saves the Galman homeworld. Sanada and a Galman scientist, Frausky, take off with a task force to save the Sun.
- Raging Sun: Sanada and Frausky use proton missiles and magnetic shields in an attempt to control the Sun, but their efforts fail and Frausky dies. Kodai and Yuki encounter some Galmans praying to Mother Shalbart to end the chaos in space. Kodai asks Desslar to be lenient towards the Shalbart-worshippers. Desslar disagrees, but tells Kodai that he has found a suitable planet for Earth's migration, called Phantom.
- The Way to Planet Phantom: Bolar Prime Minister Bemlayze orders destroyers sent out after the Yamato. The Yamato detects an SOS and helps a crashed ship of Mother Shalbart seekers. The Bolar forces attack with missiles and Kodai counters with Wave Motion cartridges. Bolar ships attack the Shalbart-followers' ship, but the Cosmo Tigers destroy them. Mother Shalbart appears to the crew of the Yamato, seemingly in the direction of planet Phantom.
- The Planet of lllusions: The Yamato arrives at planet Phantom and it seems to be exactly like Earth. The crew is overjoyed, but Analyzer warns them of danger but can't explain why. When Kodai and the crew land they begin seeing dead people and other impossible illusions.
- Lost Hope: Kodai contacts Desslar, who sends Major Harmeyai to investigate. Harmeyai sees a world exactly like Gamilon. Analyzer says the planet is alive, but Harmeyai doesn't listen and begins to drill into the planet to get samples. The vegetation attacks and the Galmans and Yamato escape. Domon and his pilot friend Ageha however are left behind, so they follow an image of a woman deeper into a cave tunnel. Meanwhile Desslar orders General Gustav to destroy planet Phantom.
- Goodbye Planet Phantom: Domon and Ageha meet the life force of planet Phantom. It tells them that Princess Luda of Shalbart was exiled here by the Bolar Federation, and needs them to take her off the planet since the Bolar Federation and the Galman-Gamilas Empire are about to attack. Domon and Ageha return to the Yamato with Princess Luda. When Galman General Gustav fires a proton missile at planet Phantom, the Yamato fails to stop it and Phantom is destroyed. As the Yamato departs, both Bemlayze and Desslar order their forces to pursue them.
- Battle at Scalageck: At planet Beta the Yamato discovers the wrecks of the Arizona and the Alexander, victims of Bolar attacks. Galman General Gustav arrives and demands to have Princess Luda. Kodai refuses and launches the Cosmo Tigers. Desslar calls Gustav and tells him to protect the Yamato from the Bolar fleet until Desslar himself arrives. The Bolar fleet arrives and when the Yamato is damaged, Gustav sacrifices his own fleet to protect the Yamato. Bolar reinforcements arrive, forcing the Yamato to use asteroids as a shield. Kodai orders the Yamato to charge below the Bolar fleet where it destroys them with Wave Motion cartridges and smokestack missiles. The Yamato leaves to take Princess Luda back to Shalbart.
- The Secret of Shalbart: Princess Luda leads the Yamato through a hidden space passage towards Shalbart, which turns out to be Earth-like and inhabited by simple non-technological humans. Unfortunately Desslar and the Bolar Federation have both followed them to Shalbart as well. The Bolar ships begin attacking and the Yamato tries to defend the weaponless natives. Desslok fires a Hyper Desslar Cannon which destroys the Bolar fleet in a single shot. Princess Luda gives the Yamato the HydroCosmogen gun in order to repair the Sun, after which she ascends to become the new Mother Shalbart. Desslar realizes that Shalbart is not a danger to Galman-Gamilon, and so loses interest and leaves. The Yamato leaves for Earth to attempt to save it with the the gift from Shalbart.
- Yamato, Shoot the Sun!: The Yamato returns to the Solar System and is about to fire the HydroCosmogen gun to repair the Sun, when the Bolar fleet warps in and attacks, followed by Bemlayze in a giant mechanical Space Fortress. Bemlayze attacks with Black Hole bombs and the HydroCosmogen gun is damaged. Desslar appears and attempts to defeat Bemlayze but his ships are no match for the Black Hole bombs. When Domon is injured trying to repair the HydroCosmogen gun, Ageha becomes upset and flies his Cosmo Tiger into the Bolar Space Fortress. Desslar fires the Hyper Desslar Cannon and the Space Fortress is destroyed. Domon manages to fix the HydroCosmogen gun and when Kodai fires it, the Sun is repaired. Domon dies from his wounds, and Princess Luda (now Mother Shalbart) takes Ageha's soul back to Shalbart. Desslar says farewell and the Yamato returns to Earth.