Across the span of the 20th century, environmental catastrophes give rise to giant monsters and superhumans, known as mutants, who are recruited into the Earth Defense Force (EDF) to defend humanity. In Antarctica, during a fierce clash with the original Gotengo, the king of the monsters, Godzilla, is trapped beneath the ice after a cave-in triggered by missiles launched from the Gotengo by Captain Douglas Gordon. This grim escape into legend sets the stage for decades of uneasy peace and renewed threat, as the EDF battles not only monsters but the evolving creatures that roam the planet.
Years later, an upgraded Gotengo, now helmed by Gordon himself, defeats the sea-dwelling Manda in the English Channel near Normandy. The victory leaves the ship badly battered and Gordon suspended from the EDF. Enter Ensign Shin’ichi Ôzaki, who is tasked with guarding a UN biologist, Dr. Miyuki Otonashi as she studies a mummified creature. The two are suddenly teleported to Infant Island, where they meet the Shobijin—the priestesses of Mothra—who reveal that the mummified thing is Gigan, an ancient extraterrestrial cyborg sent to devastate Earth. The Shobijin warn that a clash between forces of good and evil is looming, and Ozaki must choose a side.
The threat materializes as a chorus of colossal assaults: Rodan strikes New York City, Zilla invades Sydney, Anguirus bombs Shanghai, King Caesar attacks Okinawa, Kamacuras sweeps Paris, Kumonga menaces Monument Valley, Ebirah hits Tokai, and Hedorah scorches Los Angeles. Meanwhile, Minilla, Godzilla’s son, is discovered in Aokigahara by Kenta Taguchi and his grandfather Samon Taguchi. The EDF fights to hold back the onslaught, but the Xiliens soon appear, their mothership looming over Tokyo. The aliens claim they have eliminated the monsters as a goodwill gesture and offer help against a looming runaway white-dwarf star called Gorath, proposing a peace pact with humanity.
Distrust rises as Ozaki, Miyuki, and Miyuki’s sister Anna Otonashi uncover the grim truth: Gorath’s showpiece is a hologram, and the Xiliens have replaced several EDF members and Naotarô Daigo with imposters. With Gordon’s aid and the help of the mutants, the group unmasks the deception, and the Xiliens’ second-in-command—the Controller—kills his own commander to seize control. He plans to feed on humans and to bend the mutants to his will via a DNA property known as “M-base,” while waking Gigan to wipe out the EDF. The crew escapes in a repaired Gotengo, but Gigan relentlessly pursues them.
Gordon convinces the Gotengo crew to journey to Antarctica to release Godzilla, who remains immune to Xilien control thanks to his lack of M-base. Godzilla readily defeats Gigan and then engages in a rapid-fire sequence of battles as the Gotengo leads him toward Tokyo to square off with the Xiliens. After Katsunori Kazama sacrifices himself to disable a shielding barrier, the EDF crew penetrates the mothership only to be captured and brought before the Controller as he summons Gorath to Earth. Godzilla destroys Gorath just before it crashes into Tokyo, but Monster X rises from its wreckage, and the two titans clash again.
A final turn of events reveals that both Ozaki and the Controller are Keizers—superior beings born when human DNA fuses with M-base—before the Shobijin’s blessing unlocks Ozaki’s power and breaks the Controller’s hold. A fierce battle erupts, and the Controller dies as Ozaki’s energies surge to Godzilla, granting him a temporary edge to vanquish Keizer Ghidorah. Yet the victory comes at a cost: the Gotengo is shaken, and Godzilla turns his anger toward his would-be saviors.
In the tense moments that follow, Godzilla briefly shoots down the Gotengo before finally listening to his son Minilla, who calms the beast and urges forgiveness for humanity’s past transgressions. With the ship repaired and the human crew’s resolve renewed, Godzilla and Minilla retreat to the ocean, leaving the world with a wary but hopeful quiet—and a bond between father and son that endures beyond the day’s battles.
