As a teenager, Yoko discovers that she is not really an orphan when her wealthy but very strange family welcomes her home to a mansion that many claim is haunted.

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.