In 2202, three years after the Gamillas invasion of the Solar system, the people in the Solar System are finally at peace. The Earth's biosphere has been restored with the Cosmo Reverse System brought by the Yamato at the end of Space Battleship Yamato 2199. 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. Earth is set on a path of military expansion despite Starsha Iscandar's wishes of peace, and developing new forms of wave motion gun despite the agreement between Starsha and the crew of the Yamato. When a new threat called Gatlantis, also known as the White Comet Empire, starts to wreak havoc on a newly reformed galaxy, the goddess Teressa calls upon the Yamato once more in order to fight back against the new threat.