The movie begins with astronauts Glenn and Fuji on a mission to investigate a new planet called Planet X. They discover that the planet is under constant attack from a three-headed monster called Ghidorah, also known as "Monster Zero". The inhabitants of Planet X, who refer to themselves as "Xiliens," offer to exchange their advanced technology for Godzilla and Rodan, whom they believe can defeat Ghidorah and save their planet.
The Xiliens take the monsters back to Planet X, and the humans soon discover that the Xiliens are not what they seem. They have mind control technology and plan to use Godzilla and Rodan to conquer Earth. Meanwhile, on Planet X, Godzilla and Rodan are defeated by Ghidorah, who is revealed to be under the control of the Xiliens.
When Glenn and Fuji return to Earth, they learn of the Xiliens' true intentions and plan to stop them. They team up with Japanese military forces to launch an attack on the alien's base. Godzilla, Rodan, and Ghidorah eventually end up back on Earth, where a final battle takes place.
The movie ends with Godzilla and Rodan saving Earth and the people of Planet X, who have turned against their alien leaders. The Xiliens attempt to flee back to their home planet but are destroyed by their own technology. Godzilla and Rodan are hailed as heroes, and the humans bid them farewell as they return to the ocean and sky respectively.