In the year 2199, the Gamilon race declares war on humans, intent on taking Earth for themselves. The fighters on Earth do everything in their might to keep the planet stable, but alien technology proves to be far too advanced, and the resulting destruction renders the surface of planet Earth completely uninhabitable. The underground shelters are also becoming weak, and if nothing changes, humans will become extinct in less than a year. But just when all seems lost, Queen Starsha from the planet Iscandar offers a helping hand. The key to victory lies in the Cosmo-Cleaner D, which can eliminate the radiation that Earth is suffering from. However, the only way to get a hold of this life-saving device is if someone from Earth goes to Iscandar―148,000 light years away―to retrieve it. The problem is, they have less than a year before time runs out. The fate of the entire human race lies in the hands of the crew of a salvaged WWII craft, the Space Battleship Yamato.

In the year 2199, Earth is a mere shell of its former glory after a vicious bombardment by the Gamilas Empire. The inhabitants have been forced underground to escape the irradiated surface, but the deadly radiation inches closer and closer to the retreating population. With only one year before complete and utter extermination, time is fast running out and hope is in short supply. So far, any attempt to escape or retaliate has been instantly annihilated by the alien empire—until an emergency transmission from the planet Iscandar in a neighboring galaxy offers a glimmer of hope to save the doomed planet. Covertly, Earth's Self Defense Force constructs a faster than light engine for a journey to Iscandar. Armed with new weapons and a determined crew of fearless navy men, the World War II era battleship Yamato is reborn as Space Battleship Yamato. She and her crew set out on a perilous journey across the stars to save their home and the entire human race. [Written by MAL Rewrite]

In the year 2201, one year after the Yamato saved Earth from radioactive contamination, a new threat emerges. The Yamato makes its final journey to save the Earth from this new threat. Earth has almost recovered from the battle against Gamilus, and reconstruction has expanded to the other planets. When former Yamato crew-mates discover a strange, garbled message that seems to be coming from a white comet headed towards Earth, they hijack their old space fortress and begin a new battle. (Source: AnimeNfo)

The Black Nebula Empire attacks Earth and threatens to blow up the planet with a bomb they placed on Earth if counter attacked. Earths hopes rest on the Yamato crew as they go to the Black Nebula Planet and try to find a way to difuse the bomb before it's too late. (Source: ANN)