In Antarctica, Godzilla is entrapped in ice after a battle with the original . In the year 203X, environmental disasters cause the appearance of giant monsters and super-humans, dubbed "mutants", who are then recruited into the Earth Defense Force (EDF) to battle the monsters. An upgraded Gotengo, commanded by Captain Gordon, battles and destroys , but in the process, the ship is wrecked and Gordon is suspended from the EDF.
Mutant soldier Shinichi Ozaki is tasked with guarding a biologist, Dr. Miyuki Otonashi, who's sent to study a mummified monster. They are teleported to Infant Island where they encounter the Shobijin, fairies of , who reveal the mummified monster as , an alien robot sent to destroy the Earth who was ultimately defeated by Mothra. They warn that a battle between good and evil will happen soon and that Ozaki must choose a side. Giant monsters begin attacking several major cities. The EDF engage the creatures, who mysteriously vanish at the same moment when an alien mother ship appears over . The aliens, named Xiliens, warn that an incoming planet called "" will soon impact the Earth. A peace pact is signed between Earth and the Xiliens. Meanwhile, Minilla, Godzilla's son, is found in the forest by a boy and his grandfather.
Distrusting the Xiliens, Ozaki, Miyuki, and her sister, Anna discovers that Gorath is actually a hologram, the Xiliens unleashed the monsters and also replaced several members of the EDF with android duplicates. After exposing them on television, the Xiliens Controller reveals their actual plans to use mankind as a food source. The Controller assumes control of all of the mutants except Ozaki. The others escape while The Controller awakens Gigan and unleashes it along with the other monsters once again. Gordon convinces the group that only Godzilla can defeat the monsters and the group departs to Antarctica. Gigan is sent to destroy them but is easily destroyed by Godzilla. The Gotengo then guides Godzilla into battle with the other monsters and returns to Tokyo to engage the Xiliens. After penetrating the mother ship, the group is captured and taken to the controller.
Godzilla destroys Gorath just before it crashes, unleashing . An upgraded Gigan aids Monster X but is intercepted by Mothra, who both perish in the end. The Controller reveals that both he and Ozaki are "Keizer's", super-beings with unimaginable power, and attempts to control Ozaki but is stopped by Miyuki. Ozaki defeats the Controller, who sets the ship to self-destruct. The humans escape in the Gotengo moments before the mother ship explodes. Godzilla and Monster X continue their battle but he transforms into his true form, Keizer Ghidorah. Keizer Ghidorah initially gets the upper-hand but Godzilla emerges victorious in the end. Minilla shows up at the scene and convinces Godzilla not to destroy the Gotengo. The survivors watch Godzilla and Minilla return to the ocean.