In the 1960s, two astronauts, Fuji and Glenn, are sent to investigate the surface of the mysterious “Planet X”. After landing, Glenn vanishes. A flat voice comes over the communications link and instructs Fuji down into subterranean corridors to the office of the Controller of the Xians, where Fuji finds Glenn. The surface of the planet is attacked by a monster that Fuji and Glenn recognize as King Ghidorah, known to the Xians as Monster Zero. The Controller requests to borrow Godzilla and Rodan, known to the Xians as Monster Zero-One and Monster Zero-Two. In return, Planet X will give humanity a wonder drug that can cure all diseases. The astronauts then return home with the proposal.
Meanwhile, Fuji’s sister’s boyfriend, Tetsuo, has invented a personal alarm he thinks women could use if they’re attacked. Miss Namikawa makes an offer to buy the alarm as an educational device, although, her boss wants the device only to be destroyed. Fuji and Glenn tell their superiors about the offer from Planet X. Scientists begin searching for Godzilla and Rodan. The Controller of Planet X suddenly makes an appearance on Earth, and both Glenn (who is dating Miss Namikawa) and Fuji become suspicious of Planet X. The Xians find and transport Godzilla and Rodan to Planet X to battle King Ghidorah. Glenn, Fuji and Dr. Sakurai are too taken to receive a box the Controller says contains the formula for the miracle drug.
Back home, the box (containing a tape) is taken to a special meeting and it is loaded to play however, the Controller’s voice comes on, giving Earth an ultimatum of twenty four hours to surrender to the Xians. After being blown off by Miss Namikawa, Tetsuo follow her, but is captured by the Xians. Glenn eventually discovers Namikawa is from Planet X and all their women are virtually identical. The Xians lock him in the same cell as Tetsuo. Before she is disintegrated, Namikawa gives Glenn a letter which reveals the Xians’ weakness: the sound from Tetsuo’s alarm. Tetsuo uses his prototype and he and Glenn manage to escape. Twenty four hours pass and Godzilla, Rodan, and King Ghidorah are unleashed by the Xians onto Japan.
Glenn and Testuo explain the Xians’ weakness to Dr. Sakurai and arrangements are made to extend the noise. The monsters are no longer under the Xians’ control and their spacecrafts explode. Godzilla and Rodan attack Ghidorah, forcing all three to fall into the sea. Ghidorah then retreats back into space. Glenn and Fuji are to be sent back to Planet X as ambassadors to seek peaceful relations.