The movie is set in the far-off future of 1999, where humanity has taken significant strides in space travel, and most of the world's monsters are contained on a secluded island called Monsterland. The island is used as a research facility by the United Nations Science Committee, with its massive underground base containing intelligent security systems and advanced technology.
However, the alien race called Kilaaks takes over the minds of the Monsterland scientists and unleashes all of the monsters to wreak havoc across the world's major cities. Godzilla, Mothra, Rodan, Anguirus, Gorosaurus, Kumonga, and Manda all obey the Kilaaks, who promise to share their "advanced civilization" with humanity, and Japan sends the X-2 to the Kilaaks' lunar base to end the threat before all life on Earth is destroyed.
The crew of the X-2 includes Captain Katsuo Yamabe (Akira Kubo) and astronauts Yoshio Tsuchiya, Yosuke Natsuki, and Yasuhiko Saijo. They discover the Kilaaks' base within a moon crater, where the Kilaak Queen (Kyoko Ai) awaits them. The Queen and her attendants mind-control the astronauts, but the remaining scientists discover through telemetry that the aliens' weakness is that they can only focus on controlling one monster at a time, and destroying the Kilaak transmitter frees them from the alien's control.
The scientists send the monsters to attack the Kilaaks' base and destroy the transmitter, restoring the monsters back to their island-bound captivity. As the X-2 departs, Godzilla and company return home, and the Kilaaks' lunar base blows up, indicating their defeat. The remaining Monsters now have a new mission to defend Earth from any future threats.