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.

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.

Kodai and the Yamato are forced to make a nearly impossible decision. Source: crunchyroll

The continued search for the planet Terezart leads the Yamato through a strange spatial phenomenon. Source: crunchyroll

An adversary from Kodai’s past forces Yamato into a dangerous game of cat and mouse. Source: crunchyroll

The crew of the Yamato are in dire straits when a supposed onboard spy compromises their location. Source: crunchyroll

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

The time has come to break the barrier surrounding Terezart, but Zurvival will fight to impede the Yamato’s progress any way that he can. Source: crunchyroll

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

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

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. Source: crunchyroll

The Inferno Cannon fires, but that’s the least of Andromeda’s problems. Source: crunchyroll

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

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

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. Source: crunchyroll

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

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

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

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

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