Following the aftermath of Mechagodzilla's destruction, humanity seeks a permanent defense against Godzilla. The
United Nations Godzilla Countermeasure Center initiates two covert programs: Project M.O.G.U.E.R.A., which constructs a massive, heavily armed robot to eliminate the titan, and Project T, spearheaded by telepathic psychic Miki Saegusa. Miki is equipped with a psychic-control device designed to mentally dominate Godzilla and bend him to human will. Meanwhile, unknown to Earth’s forces, G-cells carried into the cosmos by Mothra and Biollante are mutated by a black hole and cosmic radiation, rapidly evolving into SpaceGodzilla—a malevolent, crystal-armored doppelgänger driven by an insatiable, deep-seated hatred for his terrestrial counterpart.SpaceGodzilla begins his devastating trajectory toward Earth, obliterating NASA's space station and destroying the Mobile Operation Command Car during Miki's field test of Project T, where the mind-control crystal is shattered by Godzilla. Simultaneously, a mysterious entity known as the Cosmos warns humanity of the impending apocalypse. As SpaceGodzilla touches down on Birth Island, he effortlessly defeats Godzilla, entrapping his adoptive infant son, Little Godzilla, in a cage of jagged pink energy crystals. SpaceGodzilla then flies to Fukuoka, utilizing the city's towering Fukuoka Tower as a massive energy capacitor to amplify his devastating cosmic powers and construct an impenetrable crystal fortress.With Godzilla tracking his rival to the mainland, the newly launched mecha M.O.G.U.E.R.A. is deployed to intercept both monsters. Realizing that SpaceGodzilla poses an
existential threat to the entire planet, the human pilots and the military forge an uneasy, desperate alliance with Godzilla. During the climactic, multi-sided battle in the ruined heart of Fukuoka, M.O.G.U.E.R.A. sustains severe damage but manages to separate into its component vehicles, allowing the pilots to destroy the crystal tower powering SpaceGodzilla's shield. Deprived of his primary energy source, the cosmic monster weakens significantly. Godzilla seizes the tactical advantage, unleashing his ultimate spiral heat ray to blast through SpaceGodzilla's armor and detonate his internal core. M.O.G.U.E.R.A.’s remaining forces deliver the final blow, sacrificing themselves to completely obliterate the invader in a cataclysmic explosion. With the cosmic threat eradicated, Godzilla returns to the ocean, leaving humanity to rebuild and reflect on the fragile truce shared with the king of the monsters.