Unable to destroy Godzilla, the Earth Defense Force sends the vehicle "Gotengo" to corner Godzilla in the South Pole, burying him in ice. This freezes him and removes him as a global threat Years later, the EDF discovers a mummified space monster, sending a Mutant soldier named Ozaki as well as a UN biologist named Dr. Otanashi to research it. Soon after this, the pair meet Mothra's fairy guardians. The fairies explain that this creature is Gigan, a creature sent to ruin Earth 12,000 years prior and warn of a coming clash between good and evil.
Kaiju begin appearing everywhere, and despite defeating Ebirah, the EDF is otherwise useless. With most of the cities destroyed, the kaiju all disappear as a massive alien ship appears above Tokyo. These "Xiliens" state that they are friendly and have eradicated the monsters. They also warn of an impending asteroid, Gorath, that will hit Earth soon.
Ozaki and several others distrust the Xiliens, eventually discovering that they are actually the ones behind unleashing the kaiju to begin with, as well as replacing EDF members with robots. Their ultimate plan, is exposed on television, is to harvest mitochondria from an enslaved humanity for food. Opposed to his superior's plans, the Xilien commander's underling, known as the Regulator, assumes control of Earth's mutants, except for Ozaki. The kaiju return, with Godzilla's son Minilla being found, to and the other resistance flees to a secret area.
Gotengo captain Gordon suggests freeing Godzilla to defeat the kaiju. While returning to Antarctica, Gigan chases them. Godzilla's first act from release is defeating Gigan, then following the Gotengo. After several short battles against Xilien-controlled monsters, the Gotengo and Godzilla reach Tokyo, with the Gotengo entering the Xilien mothership.
During these battles, Ozaki's comrade Kazama scrambles the Mothership's shield at the cost of his life while Gorath crashes into Godzilla, where Monster X manifests and begins to battle Godzilla. Gigan joins Monster X's side, but Mothra engages Gigan. Rhe humans confront the Regulator, where he reveals that he and Ozaki are "Keizers," beings capable of controlling the Earth. Ozaki sides with the humans and fights against the Regulator, eventually proving victorious and flees the Mothership's destruction.
During the kaiju battle, Mothra destroys Gigan, but Monster X changes into Keizer Ghidoraj and overwhelms Godzilla with lightning and a vitality-draining bite. Ozaki lends Keizer energy to Godzilla, allowing him to win. Godzilla sets his sights on the Gotengo, but Minilla stops him.