After an alien invasion threatens to annihilate the human race, a young Japanese girl, named Milly (Anne Suzuki), travels back in time from 2084 to October 2002, and enlists the reluctant aid of skilled Tokyo gunman, named Miyamoto (Takeshi Kaneshiro), to discover and prevent the start of the war. However, trouble ensues when the two protagonists are forced to deal with a Japanese mafia boss, named Mizoguchi (Goro Kishitani), who is somehow involved in the start of the war by keeping the first alien spaceship and its alien pilot captive, while our two heroes race against the clock to find a way to stop the oncoming destruction from the vengeance-seeking alien invasion fleet on its way to Earth.

In 2199, five years after the start of the Gamilas attack on Earth, the planet has been ravaged by the aliens' radiation bombs and the remnants of humanity have fled underground. One day, former pilot Susumu Kodai discovers a capsule sent from the planet Iskandar that tells of a device that can remove the radiation from the Earth's surface. The United Nations of Space Administration rebuilds the battleship Yamato, with a new type of propulsion system - the wave motion engine. This enables it to make the long trip to Iskandar and back in hopes of saving the Earth. Within 73 days the radiation will drive the rest of humanity to extinction.