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.

Forty-two years after her first visit in Tokyo, Mothra returns to warn mankind that they must return Mechagodzilla, along with Godzilla's bones, to the sea, for the dead must not be disturbed. If not, dire consequences will follow. However, Godzilla is once again on the rampage, and Mechagodzilla is Japan's only defense.—Oliver Chu