Manga artist Gengo Odaka lands a job with the World Children's Land amusement park only to become suspicious of the organization when a garbled message is discovered on tapes. As Gengo and his team investigate, Godzilla and Anguirus quickly decipher the message and begin their own plan of action.

With no means for defeating Godzilla Earth, mankind watches as King Ghidorah, clad in a golden light, descends on the planet. The heavens and earth shake once again as the war moves to a higher dimension.

Follows the heroic efforts of the crypto-zoological agency Monarch as its members face off against a battery of god-sized monsters, including the mighty Godzilla, who collides with Mothra, Rodan, and his ultimate nemesis, the three-headed King Ghidorah. When these ancient super-species, thought to be mere myths, rise again, they all vie for supremacy, leaving humanity's very existence hanging in the balance.

Astronauts Glenn and Fuji investigate Planet X and encounter mysterious aliens known as the Xiliens, who ask Earth's people to help save their world from "Monster Zero". In exchange for borrowing Godzilla and Rodan, the Xiliens offer a cure for cancer. As Glenn investigates, he develops a romance with Miss Namikawa and uncovers the Xilien's true intentions.

At the turn of the century, all of the Earth's monsters have been rounded up and kept safely on Monsterland. Chaos erupts when a race of she-aliens known as the Kilaaks unleash the monsters across the world.

The Futurians, time-travelers from the 23rd century, arrive in Japan to warn them of the nation's destruction under Godzilla. They offer to help erase Godzilla from history by preventing his creation. With Godzilla seemingly gone, a new monster emerges as the Futurians' true intentions are revealed.

Godzilla has become a distant memory for Japan when the destruction of a US submarine raises alarms for Admiral Tachibana. His estranged daughter Yuri investigates the legend of the guardian monsters, who must rise to protect Japan against the vengeful spirits within Godzilla that seek to destroy both the nation and its people for the suffering they inflicted in the Pacific conflict.