When the last space fleet of the UN forces fight against Gamilas forces near Pluto, a mysterious spaceship make a emergency landing on Mars.

The space battleship Yamato is the human built in secret. Yamato has to trip to the planet Iscandar, 168,000 light-years away from the Earth.

Yamato has engine trouble during the test of the warp drive system. When the crew are repairing it at Jupiter, Gamilas forces attack on Yamato.

There is a Gamilas meteorite-bombs launching base in Pluto. Earth is devastated by the bombs until now. Captain Okita decides to attack on the base.

Yamato crew's opinions are opposed about Melda who survived a pilot of Gamilas forces.

Which started the war, UN or Gamilas? The question and the truth makes a gap between Kodai and Shima. Meanwhile, Dethler orders Domel to subjugate Yamato.

The planet named Bemera-4 where Yamato stopped for supply is Earth-like world. Niimi and Itou lead a mutiny to abandon Yamato's mission, and they want to let people emigrate from Earth to Bemera-4.

Yamato come back into the Solar System. And a miracle will happen to crew.