Three years have passed since the voyage to Iscandar. The Earth, revived with the use of the Cosmo Reverse System, is recovering rapidly. Meanwhile, an allied fleet of Gamillas and humanity is engaged in a battle against the mysterious Gatlantis. In the midst of the conflict, the Yamato stirs from its slumber...

The newly established Earth Federal Government is enacting rapid military expansion plans culminating in the launch of four state-of-the-art Andromeda class starships equipped with Wave Motion weapons. Meanwhile, the former crew of the Yamato gathers at Captain Okita's memorial monument and try to make sense of the unease growing among them after they all received a strange vision compelling them to man the old ship.

While Kodai has difficulty coming to terms with the knowledge of what truly happened to Earth after the restoration and the possible meaning of the vision he received, Mori struggles with her own identity, her relationship, and the fact that she wasn't called to the Yamato.

With unease, Kodai takes the position of acting captain of the Yamato and its crew as they prepare to launch the ship, thus rebelling against the Earth Federal Government.

The Yamato reaches the asteroid belt beyond Mars but must soon face a powerful deterrent to their rebellion in the form of the Andromeda, one of the newly launched flagships of the Earth Federation Fleet.

The Yamato comes across a survivor from a Gatlantis attack on the eleventh planet, and the crew decides to go off course from their journey to Telezart to rescue any survivors.

Trapped under rubble and deprived of sensors, the crew focuses on repairing the damage when an alarming report arrives from the outside. The Gatlantis are amassing thousands of ships in orbit around the artificial sun, and Analyzer's conclusion forces Kodai to contemplate a dramatic outcome.

The Yamato rendezvous with allied Gamillas ships on the volcanic planet Stravase in order to transfer the civilians rescued from the ruins of the eleventh planet.

Zworder, Emperor of the Gatlantis, appears in front of Kodai and forces a dilemma.

Yamato resumes its voyage to Terezart, but soon encounters a swarm of space-born organisms that threaten the stability of the crew and the ship. Teresa reaches out once more. Zworder dispatches a new ally of his own and an old adversary of Yamato to defeat the Earth vessel.

The fallen leader of the Great Garmillas Empire, Abelt Dessler, is dispatched by Emperor Zworder to destroy a rogue Gatlantis fleet and hunt down the Yamato. As his old adversaries attempt to escape, Dessler takes advantage of a new opportunity.

Zworder brings the force of the White Comet directly to Yamato. Just as Katsuragi is revealed as an infiltrator and attempts to make her escape, she discovers a disturbing secret about her true nature.

The crew’s hard-fought journey to reach Telezart comes to a head. With heavy enemy presence in the area, Yamato is driven into a corner, and available options are dwindling.

The Yamato works under fire to break up the rocky crust imprisoning the planet Terezart, while Cosmo Marines and fighter pilots fight against Gatlantis' massively armed ground forces. Kodai, Sanada, and Saito venture under the surface of Terezart to meet the goddess Teresa.

The Yamato has its purpose, and Desler’s tragic past is revealed.

Keyman faces his toughest decision yet—does he side with Desler or with the Yamato?

The Gatlantean Fleet is pushing toward Earth, and it’s up to the Andromeda to lead the defense. Meanwhile, the Yamato has a way to upgrade its Wave Motion Gun.

The white comet arrives at Saturn. The earth defence forces attempts to fight it.

The Yamato plummets toward an unknown planet. Time is of the essence regarding a new strategy to defeat Zworder.

An AI construct exposes Zworder’s past. His hatred of humanity and his mission to annihilate mankind finally surfaces.

A device that could stop the Gatlanteans, once and for all, is uncovered, and prompts a counterattack from Zworder along with the mobilization of Earth’s new AI-controlled fleet.

With Ginga’s assistance, Yamato is rebuilt. But can Yamato survive when one of their own is a potential spy?

While locked in battle with the Yamato, Zworder tests Keyman, Desler, and the Gamilan race.

Earth is under threat. The Yamato and its allies strike at the heart of the Comet Empire.

Zworder made his choice—the Ark of Destruction is unleashed.

Six months have passed. Kodai and Yuki wander aimlessly within a higher dimension.