Two innocent high school girls, Aki Shindo, nicknamed Ako, and Mineko Mayama, nicknamed Neko, run away from home and, along with Kaori Yashiro, whom they meet while hitchhiking, arrive at a certain beach. There, at a yacht harbor, they find Daisuke Sakuma, whom they met in town. Daisuke had come there to head to the Galapagos Islands at the request of his seniors, Yamamuro and Akira Kanno.

Manga artist Gengo Odaka lands a job with the World Children's Land amusement park only to become suspicious of the organization when a garbled message is discovered on tapes. As Gengo and his team investigate, Godzilla and Anguirus quickly decipher the message and begin their own plan of action.