Just as Gatlantis prepares to slaughter the Terran fleet, Wave Motion Gun shots crash through Saturn's rings and destroy a portion of the Gatlantis fleet. Terran ships jump through the rocks and begin their assault, as more de-warp into the system. Before the fleets can fight for too long, the White Comet jumps into Saturn and destroys a chunk of it. The Wave Motion fleet scattered, the Yamato attempts to use the Wave Motion Gun to disable the White Comet, but are instead knocked out of commission and dragged into the white abyss.

Gatlantis have begun their second phase of invading the Solar System, by sending an advanced force to Saturn. The UNCF fleet moves to defend Saturn, but are slowly overwhelmed. On Earth, the President of Terra declares open war with Gatlantis. Admiral Yamanami, in charge of Andromeda, takes his fleets and counter-attacks against Gatlantis.

Keyman finds himself questioning his choices, and goes back to Teresa to seek guidance. Albelt also finds that he himself requires answers, and also seeks Teresa's counsel, even if he does not necessarily want it. Keyman, now having a new purpose, frees the captives aboard Dessler's ship and flees back to the Yamato.

Teresa reads through Desslers mind, dredging up old memories from a time long passed. Kodai sneaks up behind him, intent on ending him for good. Keyman arrives minutes later, wanting to find out the truth. It is revealed that he himself is a Dessler, and nephew to Albelt Dessler. Keyman turns his gun on Kodai and knocks him unconscious.

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

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

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

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

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.

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 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.

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.

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.

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.

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.

A planet called Telezart comes under attack by a race known as the Gatlantis, who wish to conquer the world and use its power for their own gain. Meanwhile, Earth and Garmillas, now allies after their ten year war, fight side by side to retake a world lost. The Yamato crew are angered by the revelation of the Andromeda class battleship. The crew receive a vision from a planet called Telezart, calling for their aid.