Inventor Goro Ibuki creates a humanoid robot named Jet Jaguar. It is soon seized by an undersea race of people called the Seatopians. Using Jet Jaguar as a guide, the Seatopians send Megalon as vengeance for the nuclear tests that have devastated their society.

An Okinawan prophecy that foretells the destruction of the Earth is seeming fulfilled when Godzilla emerges to return to his destructive roots. But not all is what it seems after Godzilla breaks his ally Anguirus's jaw. Matters are further complicated when a second Godzilla emerges, revealing the doppelgänger as a mechanical weapon.