In 1932, the Japanese Army investigates a mysterious meteorite crash in Manchuria, and discovers a strange material that produces a previously unknown kind of energy. The mineral is later used during the Second World War to power a massive submersible battleship Ra, which is built to revitalize the war effort. Shortly before the launch, a young woman named Annette approaches the officers of the Ra and implores them not to use the battlesub. She says the material was sent by subterranean humans to test the surface dwellers right to live, and by using it as a weapon of war they are sealing the human race’s fate. The Ra is launched in the twilight days of the war, and shortly after the bombing of Hiroshima the Ra encounters the American battlesub Liberty, whose crew has been tricked into fighting the Ra by Annette’s former partner and friend Avatar, whose appraisal of the human race is much more negative than her counterpart. Annette stops Avatar with a blast of mental energy, but the Ra and Liberty destroy each other. Annette and the Ra’s first officer are the only survivors. Fifty years later, an unaged Annette and the grandson of the Ra’s captain, Go Arisake, are part of a UN team sent to investigate microwaves being generated at the South Pole. It proves to be a prelude to a massive attack from below the Earth, led by Avatar, that will culminate in the complete destruction of the surface humans. However, Go discovers his grandfather’s old ship has been found and rebuild as humanity’s last line of the defense, commanded by his believed to be dead father, as the final battle to defend Earth begins.