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 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 civillians rescued from the ruins of the eleventh planet.

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

The continued search for the planet Telezart leads the Yamato through a strange spatial phenomenon.

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

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

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.

Kodai and Yuki return to a seemingly empty Yamato. Attempts to locate the crew are hindered by a foe who can control memories.