At the close of the 20th century, all of the Earth’s kaiju have been collected by the United Nations Science Committee and confined in an area known as Monsterland, located in the Ogasawara island chain. A special control centre is constructed underneath the island to ensure that the monsters stay secure, and to serve as a research facility to study them.
When communications with Monsterland are suddenly and mysteriously severed, and all of the monsters begin attacking world capitals, Dr. Yoshida of the UNSC orders Captain Yamabe and the crew of his spaceship, Moonlight SY-3, to investigate Ogasawara. There, they discover that the scientists, led by Dr. Otani, have become mind-controlled slaves of a feminine alien race identifying themselves as the Kilaaks, who reveal that they are in control of the monsters. Their leader demands that the human race surrender, or face total annihilation.
Godzilla attacks New York City, Rodan invades Moscow, Mothra (a larvae offspring) lays waste to Beijing, Gorosaurus (wrongly identified as Baragon) destroys Paris, and Manda attacks London. These attacks were set in to motion to draw attention away from Japan, so that the aliens can establish an underground stronghold near Mt. Fuji in Japan. The Kilaaks then turn their next major attack on to Tokyo and, without serious opposition, become arrogant in their aims, until the UNSC discover that the Kilaaks have switched to broadcasting the control signals from their base under the Moon’s surface. In a desperate battle, the crew of the SY-3 destroys the Kilaak’s lunar outpost and returns the alien control system to Earth.
With all of the monsters under the control of the UNSC, the Kilaaks unleash their hidden weapon, King Ghidorah. The three-headed space monster is dispatched to protect the alien stronghold at Mt. Fuji, and battles Godzilla, Minilla, Mothra, Rodan, Gorosaurus, Anguirus, and Kumonga (Manda, Baragon and an unnamed Varan are also present but do not take part in the battle). While seemingly invincible, King Ghidorah is eventually overpowered by the combined strength of the Earth monsters and is killed. Refusing to admit defeat, the Kilaaks produce their trump card, a burning monster they call the Fire Dragon, which begins to torch cities and destroys the control center on Ogasawara. Suddenly, Godzilla attacks and destroys the Kilaak’s underground base, revealing that the Earth’s monsters instinctively know who their enemies are. Captain Yamabe then pursues the Fire Dragon in the SY-3, and narrowly achieves victory for the human race. The Fire Dragon is revealed to be a flaming Kilaak saucer and is destroyed. Godzilla and the other monsters are eventually returned to Monsterland to live in peace.