Humanity's desperate battle to reclaim the Earth from Godzilla continues. The key to defeating the King of the Monsters may be Mechagodzilla, a robotic weapon thought to have been lost nearly 20,000 years ago.

A submarine expedition to salvage the remains of Mechagodzilla is thwarted by a massive dinosaur named Titanosaurus. An Interpol investigation leads biologist Ichinose to uncover the work of Dr. Mafune and his mysterious daughter Katsura. Aligned with the Black Hole Aliens, Katsura's life becomes entwined with the resurrected machine.

Mothra and her fairies return to Japan to warn mankind that they must return Kiryu to the sea, for the dead must not be disturbed. However Godzilla has survived to menace Japan leaving Kiryu as the nation's only defense.

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.