In the year 2199, alien beings attack the last of Earth’s space fleet who are protecting a secret mission. Ace pilot Susumu Kodai retrieves an item on Mars that could save the human race, but learns tragic news about his brother.

Using the warp gate, the Yamato must bypass the planet Balun. But they’ll have to punch through a massive Gamilan fleet if they want to arrive at the Large Magellanic Cloud in one piece.

The Gamilans set their ambush into motion. The two commanders, Domel and Okita, vie for ultimate victory and survival.

With a Wave Motion Gun in Gamilan possession, the Yamato’s only option is to take the fight to Gamilas’ capital. Meanwhile, Kodai is given permission to rescue Yuki.

En route back to Earth, the crew of the Yamato have a final confrontation with Desler.