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.

Ichiro Miki is a child living in the industrial district of Kawasaki, where his parents' constant struggle to make ends meet often leaves the schoolboy alone. Constantly teased by a bully nicknamed Gabara, his only friends are toy consultant Shinpei and fellow classmate Sachiko. Ichiro turns to escapist dreams of Monster Island where he befriends the equally bullied Minilla.

After the previous Godzilla attack, a miniature arms race ensues to collect his cells. Concerned over Godzilla's possible return, the Japanese government uses the cells to create a new bio-weapon, ANEB (Anti-Nuclear Energy Bacteria). They seeks the aid of geneticist Genshiro Shiragami, who's experiments result in a new mutation.