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.

Mothra's dark counterpart, Battra, emerges to eliminate humanity on behalf of the Earth. Two tiny fairies called the Cosmos offer their help by calling Mothra to battle the creature. Unfortunately a meteorite has awoken a hibernating Godzilla as a three way battle for the Earth begins.

Journalists Ichiro Sakai and Junko cover the wreckage of a typhoon when an enormous egg is found and claimed by greedy entrepreneurs. Mothra's fairies arrive and are aided by the journalists in a plea for its return. As their requests are denied, Godzilla arises near Nagoya and the people of Infant Island must decide if they are willing to answer Japan's own pleas for help.