Three years after the war against the Gamilas, Earth has rebuilt its surface and grown complacent, its people distracted by material comfort. The great battleship Yamato, once the savior of humanity, lies decommissioned and forgotten. Meanwhile, a white comet of unnatural origin races through space, and a mysterious message pleading for help is received by former crew members Shima and Sanada. The sender is a woman named Teresa, held captive on the distant planet Telezart. Convinced that a new cosmic threat is real and that Earth’s leadership refuses to act, Susumu Kodai reunites his old comrades from the Yamato. Defying direct orders and risking charges of mutiny, they secretly take the Yamato from its dock and set course for Telezart.

On Telezart, after fierce fighting against the White Comet Empire’s forces, Kodai and his crew free Teresa. She reveals that she is the last of an anti‑matter race and that the advancing white comet conceals a mobile fortress‑city called Gatlantis, commanded by the absolute ruler Zordar. The empire’s next target is Earth. Teresa cannot join them physically, for contact with normal matter would annihilate her, but she lends her spiritual support and vanishes. Racing back toward Earth, the Yamato encounters the revived Gamilas leader Dessler, who has been granted new power by the empire. After a brutal battle, Dessler—mortally wounded and disillusioned—reveals the comet’s weak point: its spiral core. He then asks Kodai’s forgiveness and dies.

The Earth Defense Fleet, led by the new super‑battleship Andromeda, engages the White Comet Empire’s vanguard but is annihilated when the comet itself appears. The Yamato arrives and fires its wave‑motion gun into the comet’s core, dispersing the outer gas. But within the glowing remnants, the true Gatlantis fortress emerges. A desperate, grinding battle follows. One by one, the Yamato’s crew falls: the doctor Sado, the robot Analyzer, Captain Hijikata, and even Kodai’s fiancée Yuki Mori. Grieving but resolute, Kodai takes command. He leads a small strike team into Gatlantis, where science officer Sanada and space marine leader Saito sacrifice themselves to destroy the fortress’s power core. Yet from the wreckage an even larger battleship rises, dwarfing the Yamato. Zordar proclaims himself the master of the universe.

With his ship crippled and his crew decimated, Kodai communes with the spirit of Captain Okita, who tells him that human life itself is the final weapon against evil. Kodai orders all remaining survivors to abandon ship. They protest, but he convinces them that his death will give Earth a future. Alone at the helm, he steers the Yamato on a collision course with Zordar’s vessel. Teresa appears one last time, inspired to give her anti‑matter body to amplify the impact. The Yamato vanishes in a blinding flash, taking the enemy with it. Earth is saved, but the ship and most of its heroic crew are gone forever.