ฮะรุโอะกับเพื่อนๆ ติดต่อชนเผ่าพื้นเมืองฮูตูอาบนโลก พวกเขาวางแผนเดินทางไปยังศูนย์พัฒนาเมคาก็อดซิลล่าเพื่อหาวิธีโค่นก็อดซิลล่าให้ได้
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.
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.