The water planet Aquarius is heading towards Earth after flooding the home planet of the warrior race of the Dinguil. The Dinguil use warp technology to make the planet move towards Earth faster than usual. The warrior race plans to flood Earth and make it their new home. When Earth learns of this, they make plans to evacuate humanity. Unfortunately, the Dinguil destroy the evacuation fleets. The space battleship Yamato, under the newly revived Jyuzo Okita (who seemingly died in the first season of the original series) now has to fight the Dinguil and stop Aquarius from flooding the Earth.