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A scientist named Dr. James Bowen and his two colleagues, Dr. Sueko Togami and Dr. Kawachi, are studying the effects of radiation on survivors from the Hiroshima bombing. During his studies, Dr. Bowen stumbles across a small wild boy roaming the streets of Hiroshima. Bowen begins to study the child and is amazed when he discovers that the boy is in fact the revived Frankenstein monster, regrown from a dissected heart that was then mutated by the atomic bomb's radiation. However, the small child quickly grows in size and cunning, as it begins to prey on the livestock and pets in the area as a means of food. Upon learning of the creature, and his rapid and growth, the J.S.D.F. becomes worried if the monster might turn on a more abundant source of food: human beings.
Meanwhile, Godzilla is discovered trapped in ice in the Bering Sea. The SDF decides to free the nuclear menace and lure the him to Japan, where he will hopefully fight and kill the Frankenstein monster. Taking action, the military breaks the icy prison from around the creature and lures Godzilla to the Japanese coast with ships. Once there, a series of towers with light beacons on the mainland lead the atomic dragon to the Mt. Fuji area.
At Fuji, the nuclear menace spots Dr. Sueko, but before any harm can come to her Frankenstein rushes to the women's rescue and does battle with reptile. Frankenstein begins a hit and run type of battle with Godzilla, striking the dinosaur then retreating back into Fuji forest. The two titans war is interrupted, though, by a series of volcanic fissures, as one swallows Frankenstein while another causes a great flood which knocks Godzilla backwards into a raging river and is washed away by the current, his final fate is unknown.
Influenced by the concept of the giant Frankenstein monster from the King Kong vs. Frankenstein/King Kong vs. Prometheus story, Toho planned on making Frankenstein vs. Godzilla as a follow up to King Kong vs. Godzilla. Written in 1963 and planned for a 1964 release, the story dealt with the heart of the original Frankenstein monster becoming irradiated and growing into a Frankenstein-monster giant. Afraid the giant would start eating people, Godzilla would be freed from an icy prison by the JSDF and goaded into a fight with the monster in hopes of killing him. Even though King Kong vs. Godzilla had already been made with Godzilla escaping from an iceberg that he was trapped in at the end of Godzilla Raids Again, script writer Kaoru Mabuchi (a.k.a. Takeshi Kimura) thought with Godzilla disappearing into the ocean at the end of that film, that the idea of Godzilla becoming frozen in the North Sea into another icy prison could still work. The story would end with Godzilla disappearing into a raging river flow, while the Frankenstein giant disappears into magma.
Toho thought the story would not make any sense because the JSDF are trying to get Godzilla (who was still a villain at this point) to kill Frankenstein because they are afraid Frankenstein will start eating humans. So the idea was dropped and Mothra was brought in as Godzilla next opponent for the film Mothra vs. Godzilla. Toho didn't give up on the Frankenstein giant idea. In 1965, the monster would appear battling a new monster opponent named Baragon in the film Frankenstein vs. Baragon, which used a lot of concept ideas as well as the same characters, such as Dr. Bowen, from this story treatment.