Set three years after the events of the first film, Yamato must protect Earth from another tyrannical alien race in the form of the White Comet Empire, who prove to be a much graver threat.

This same storyline would be reused and expanded on later in the same year on TV in Space Battleship Yamato II, albeit with a different ending.

Meanwhile in the distant reaches of space, the tyrannical White Comet Empire led by the Emperor Zordar sets its sights on Earth to conquer and enslave mankind.

Kodai and the crew believe that the world has become too complacent with their newfound peace, feeling that people have taken for granted Yamato's sacrifices.

This feeling is further bolstered by the christening of the Earth Defense Force's newest state-of-the-art flagship Andromeda, which will succeed Yamato.

When Yamato's crew is informed that it will decommissioned, Kodai inspires them to mutiny and seek the source of the message themselves.

Encountering a distress signal, the crew rescues Captain Ryu Hijikata from the wreckage of a patrol fleet that had just been attacked by Comet Empire forces.

She explains that she is the sole survivor of her kind who had been wiped out by the Empire, and that the Comet itself conceals a base inside.

Yamato takes aim and fires at the Comet's spiral core with the Wave Motion Gun, seemingly destroying it.

Kodai, joined by Sanada and the space marines, pilots a fighter and leads the Black Tigers to infiltrate Gatlantis.

The alien base cracks open, revealing a massive battleship hidden inside that dwarfs Yamato.

Shima and the others realize his intentions and protest but Kodai convinces them, stating that by sacrificing himself, he will not truly die as Earth will live.

In 1977 the first film of the series, Space Battleship Yamato, outperformed Star Wars at the Japanese box office.