Moments after an atomic bomb falls over Hiroshima, a secret Japanese submarine sails into battle against its American counterpart, and both are lost to history. Some fifty years later, a special UN task force sent to investigate unusual phenomena in Antarctica is threatened by a mysterious black cylinder.

The incident in the Antarctic is only the first round in a cataclysmic battle of wills between two descendants of an ancient race dwelling within the Earth. Standing against them is a single, amazing ship, the RA, a Yamato-class battle sub secretly rebuilt after its supposed destruction in World War II.