The year is 2199. The human race has been crushed in their war with the Gamilos, driven into underground cities by the invader's assault. Scientists estimate they have only a year left. The young officers Susumu Kodai and Daisuke Shima receive a mysterious capsule from a ship that made an emergency landing on Mars and return with it to Earth. It contains humanity's last hope: the planet Iscandar on the other side of the Magellan Galaxy has the technology to defeat the Gamilos and restore the planet. The space battleship Yamato is entrusted with this task, but they have only one year before humanity ends.
It is the year 2202, three Years after the war with Gamillas, the people in the Solar System are finally at peace once again and the Earth has been restored back to life. With the end of the war, there is a peace treaty between Earth and Gamillas which will strengthen their military bond and secure true peace. In addition to the reconstruction of Earth, the joint forces form a new intergalactic defense fleet with a new ship, Andromeda, to be its new symbol of power. Due to these advancements, the Earth is going on a path of military expansion despite Starsha Iscandar's wishes of peace. But when a new threat called the Gatlantis starts to wreak havoc to a newly reformed galaxy, the Goddess Teressa calls upon the Yamato once more in order to fight back against the new threat.