Set in the year 2199, an alien race known as the "Gamilas" unleash radioactive meteorite
bombs on Earth, rendering the planet's surface uninhabitable. Humanity has retreated
into deep underground cities, but the radioactivity is slowly affecting them as well,
with mankind's extinction estimated in one year. Earth's space fleet is hopelessly
outclassed by the Gamilas and all seems lost until a message capsule from a mysterious
crashed spaceship is retrieved on Mars. The capsule yields blueprints for a
faster-than-light engine and an offering of help from Queen Starsha of the planet
Iscandar in the Large Magellanic Cloud. She says that her planet has a device, the Cosmo
Cleaner D, which can cleanse Earth of its radiation damage.
The inhabitants of Earth secretly build a massive spaceship inside the ruins of the
Japanese battleship ''Yamato'', the Space Battleship Yamato for which the story is
titled. Using Starsha's blueprints, they equip the new ship with a space warp drive,
called the "wave motion engine", and a new, incredibly powerful weapon at the bow called
the "wave motion gun."
A crew of 114 departs for Iscandar in the Yamato to retrieve the radiation-removing
device and return to Earth within the one-year deadline. Along the way, they discover
the motives of their blue-skinned adversaries: the planet Gamilas, sister planet to
Iscandar, is dying; and its leader, Lord Desler, is trying to irradiate Earth enough for
his people to move there, at the expense of the "barbarians" he considers humanity to
be.