In 2199, five years after the Gamilons began an invasion of Earth, the planet has been ravaged by the aliens' bombs. The remnants of humanity have fled underground to escape the irradiated surface. One day, former pilot Susumu Kodai discovers a capsule sent from the planet Iscandar that tells of a device that can remove the radiation from the Earth's surface. The Earth Defense Force rebuilds the battleship Yamato with a new type of propulsion system to make the 148,000 light year trip to Iscandar in hopes of saving the Earth. Within one year, the radiation will drive the rest of humanity to extinction.

The film begins in the present, with its heroine, Kaoru, a grown-up woman working as a real-estate agent, while helping out the folksy proprietor of a neighborhood fishing pond. There she meets a shy girl who needs her help baiting a hook and reminds her of herself in the fourth grade.