Astronauts Glenn and Fuji investigate Planet X and encounter mysterious aliens known as the Xiliens, who ask Earth's people to help save their world from "Monster Zero". In exchange for borrowing Godzilla and Rodan, the Xiliens offer a cure for cancer. As Glenn investigates, he develops a romance with Miss Namikawa and uncovers the Xilien's true intentions.
During WWII, Germans obtain the immortal heart of Frankenstein's monster and transport it to Japan to prevent it being seized by the Allies. Kept in a Hiroshima laboratory, it is seeming lost when the United States destroys the city with the atomic bomb. Years later a wild boy is discovered wandering the streets of the city alone, born of the immortal heart.
Gaira, a humanoid sea beast spawned from the discarded cells of Frankenstein's monster, attacks the shores of Tokyo. While the Japanese military prepares to take action, Gaira's Gargantua brother, Sanda, descends from the mountains to defend his kin. A battle between good and evil ensues, leaving brothers divided and a city in ruins.
