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 of Yamato plans and launches an assault on Gatlantis-occupied Terezart. At the head of the fleet defending the planet, a Gatlantean boy struggles to come of age.

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. 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

With Yamato paralyzed by an act of sabotage, most of the crew evacuate as the ship plummets toward the White Comet, and comes to rest on a mysterious and deserted planet. Sanada and other officers are introduced to a new space battleship, and learn about Earth's increasingly drastic plans for victory. The Gatlantis share a cure for a tragic disease affecting Kato's son. Mori's memories return, but at a cost.

An AI construct exposes Zordar’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 Zordar 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?

Miru has imposed a “devil’s choice”. But Kodai rejects those choices and instead offers a surrender. "No trigger need be pulled to the end the battle," he says. As Gatlantis does not understand the concept of surrender, Miru is further enraged and fires his gun again. Meanwhile, the White Comet has reached Earth.

The Yamato, with support from the Garmillas fleet, infiltrates the White Comet in a bloody bid to reach the inner sanctum of Zordar: his throne room.

By Zordar’s will, the Ark of Destruction awakens, revealing its true form, dwarfing Earth. The crippled Yamato can no longer fight. As captain, Kodai issues the final command.

It is the year 2203, six months later. Hero's Hill is now lined with additional monuments. The true trial is about to begin.