It's the year 1999. The United Nations has established bases on the moon. All of Earth's monsters have been moved to an island called Monsterland in the Ogosawara Islands. The monsters are "locked'in" the island using new technology so they won't wreak havoc on the Earth. One day, though, the island is attacked with poison gas. The monster-control apparatus goes out of order, and the monsters escape from the island. Rodan attacks Moscow, Gorosaurus attacks Paris, Mothra attacks Bejing, and Godzilla attacks New York City. The U.N. does not know what the heck is going on, so they send the crew of the spaceship "Moonlight SY3" to investigate the island. While on Monsterland, the SY3 crew meet up with the leader of a small planet in the asteroid belt called "Kilaak." The Kilaaks are an advaced alien race (obviously), and want to establish a new scientific civilization on Earth. The Kilaaks control the monsters so they can acheive their goal. The SY3 crew engage in a gunfight with the Kilaaks, and escape the island.

The SY3 crew discover most of the control apparatuses is multiple places. Meanwhile though, Rodan, Godzilla, Manda, and Mothra attack Tokyo. The Japanese military tries to fight the monsters, but are unsuccessful. The military meets up again with Godzilla and Anguirus, and are again, unsuccessful. The SY3 crew then attack the Kilaak base on the moon, and destroy it, along with the main control apparatus that controls the monsters. All of the monsters are then brought under another control apparatus that the U.N. develops. The U.N. then sends the monsters to attack the second Kilaak base on Earth. Godzilla, Minya, Anguirus, Rodan, Gorosaurus, Mothra, Kumonga, Manda, Varan, and Baragon all march towards the Kilaaks. The Kilaaks send King Ghidorah to fight the monsters because he is a space monster. The monsters, for a while, fight a touch battle, but eventually the fight leans toward the Earth's monsters. The monsters kill Ghidorah with Minya sending out his (in)famous radioactive smoke-ring around Ghidorah's middle neck. The Kilaaks then send a "burning monster" called the "Fire Dragon" towards Earth. The Fire Dragon destroys the U.N.'s new monster control apparatus. The SY3 attacks and shoots down the Fire Dragon, only to discover that it was only a Kilaak flying saucer surrounded with a flame shield. The monsters then attack the second Kilaak base without help from the demolished U.N. control device, since they know their enemies by natural instinct. The Kilaaks have been wiped out and the Earth has been saved. The monsters return to Monsterland, and Godzilla gives a tiny wave "goodbye" to a few of the members of the U.N.