In the near future, almost a century of nuclear tests, modern warfare and unchecked scientific advances have resulted in serious damage to the earth's environment. This ripple causes an unbalance in nature and rouses a score of giant monsters from their slumber. The nations of the world set aside their petty differences when these enormous creatures become the one true threat to the survival of mankind. The United Nations forms the Earth Defense Forces in order to face this crisis head-on.
In the years before this hell-on-earth broke loose it was discovered that a new breed of people all over the globe were reaching the next stage in human evolution. Blessed with extraordinary abilities, these mutants were soon recognized for their exceptional qualities by the United Nations. They are brought together to form a special branch of the Earth Defense Forces called the M-Organization.
One of the most promising members from Japan, Shinichi Ozaki (Masahiro Matsuoka), is gifted with incredible reflexes and strength. Acknowledged by his peers as a hard-as-nails soldier, he quickly moves up in the ranks of the M-Organization. When the mummified corpse of a giant monster is sighted off the coast of Japan's northern island, Hokkaido, Ozaki is called into action. He is assigned as a bodyguard to one of the United Nations' most brilliant molecular biologists, Miyuki Otonashi (Rei Kikukawa) while she tries to uncover the riddle of this strange discovery.
Suddenly, a plague of colossal beasts appear across the planet and attack the major cities of the world. New York, Shanghai, Sydney and Paris all suffer the wrath of these monsters. During this chaos, the United Nations is further thrown into panic when the private plane of UN Secretary General Naotaro Daigo (Akira Takarada) mysteriously disappears.
The Earth Defense Forces tries desperately to maintain its operational command, but the marauding monsters prove overwhelming. In a desperate bid, Ozaki and his fellow mutant soldier Kazama (Kane Kosugi) rush headfirst into the battlefield on their special motorcycles and use their super-human strength to challenge the powerful creatures.
Suddenly, enormous flying saucers appear in the skies and cause the monsters to disappear in a beam of light. From a cluster of saucers hovering over the Earth Defense Forces headquarters in Japan, the missing Secretary General Daigo is brought back by a man who identifies himself as a being from Planet X (Kazuki Kitamura). Daigo proposes cooperation between the two worlds:
"This is a test for Mankind; a time to step up to the next stage of human progress. The Xilian technology is far more advanced than our own, but we can move forward with their help and the universe will be united. The era of the United Nation is over... now is the time to found the United Universe!"
The UN concedes to the notion, but both Ozaki and Miyuki have their doubts about the motives of the Xilians. As Miyuki's sister Anna (Maki Mizuno), an investigative reporter, seeks to uncover the aliens' true intentions, a secret call for help goes out to the Captain of the Goten (aka Atragon). Ozaki and his comrades board the undersea warship to commence the final war to save humanity!
Meanwhile, in a glacier at the South Pole, Godzilla continues to sleep peacefully...