Plot
Over the course of the 20th century, environmental disasters cause the appearance of giant monsters and superhumans, dubbed "mutants", who are then recruited into the Earth Defense Force (EDF) to battle the monsters. The strongest of these monsters is Godzilla, who becomes the EDF's greatest enemy and frequently threatens mankind over the years. In Antarctica, Godzilla is finally imprisoned under the ice during a battle with the powerful EDF warship Gotengo.
Many years later, in 2004, an upgraded Gotengo, now commanded by Captain Douglas Gordon, battles and destroys Manda in the English Channel off the coast of Normandy, but the ship sustains serious damage during the battle and Gordon is suspended from the EDF. Mutant EDF ensign Shinichi Ozaki is tasked with guarding a U.N. biologist, Dr. Miyuki Otonashi, who is sent to study a mummified monster. As they examine it, they are briefly teleported to Infant Island by the Shobijin, who reveal the mummified monster as Gigan, an extraterrestrial cyborg that attempted to destroy the Earth ten thousand years earlier, and was ultimately subdued by Mothra. They warn that a battle between good and evil will happen soon, and that Ozaki must choose a side.
Several giant monsters attack major cities around the world: Rodan attacks New York City, Zilla attacks Sydney, Anguirus attacks Shanghai, King Caesar attacks Okinawa, Kamacuras attacks Paris, Kumonga attacks Monument Valley in Arizona, and Ebirah attacks Tokai. Meanwhile, Minilla, Godzilla's son, is found in Aokigahara by Kenta Taguchi and his grandfather, Samon. The EDF engages the monsters until they mysteriously vanish, as a huge alien vessel appears over Tokyo. The aliens introduce themselves as the Xiliens, claim that they eliminated the monsters as a gesture of goodwill, and warn Earth's leaders that an incoming runaway white dwarf star called Gorath will soon impact the Earth, offering their help to destroy it.
After a peace pact is signed between humanity and the Xiliens, Ozaki, Miyuki, and Miyuki's sister Anna, a news reporter, discover that the Gorath shown by the Xiliens is a hologram and that the Xiliens have replaced several members of the EDF and U.N. secretary-general Naotaro Daigo with imposters. After the Xiliens are exposed with help from Gordon and the other mutants, the Xiliens' second-in-command, the Controller, kills his leader to assume command, revealing their plan to use humans as a food source while taking control of all the mutants, except for Ozaki, through a property in their DNA known as "M-base". The Controller also has the monsters under his control through M-base in their DNA, and awakens Gigan to wipe out the EDF. The group escapes in a repaired Gotengo, although Gigan pursues them.
Gordon convinces the Gotengo's crew to travel to Antarctica to release Godzilla, who is immune to the Xiliens' control thanks to his lack of M-base and easily defeats Gigan. The Gotengo then guides Godzilla into a series of battles with the other monsters: he defeats Zilla in Sydney, Kumonga in New Guinea, and Kamacuras in Manazuru. At Hakone, Samon, who witnesses Godzilla’s arrival with Kenta and Minilla, remarks that long ago, humanity’s actions angered Godzilla, leading to his decades of aggression. After Godzilla battles and subdues Rodan, Anguirus and Caesar at Mount Fuji, the Gotengo leads him to Tokyo to defeat the Xiliens.
Ozaki’s comrade Katsunori Kazama sacrifices himself to disable the Xilien mothership’s barrier shield, allowing the Gotengo's crew to penetrate the ship, but they are captured and brought before the Controller as he summons Gorath to Earth. After defeating Ebirah and Hedorah in Tokyo, Godzilla destroys Gorath just before it can hit the Earth, but this unleashes the Xiliens' ultimate weapon, Monster X, and the two monsters battle. A repaired and upgraded Gigan joins Monster X, but is intercepted by Mothra, who manages to destroy him once and for all.
Aboard the Xilien mothership, the Controller reveals that both he and Ozaki are superior beings known as "Keizers", powerful beings distinct from regular mutants born on rare occasions when human DNA and M-base are combined, before directly taking control of Ozaki to turn him against the group. As a fight breaks out, the Controller loses control of Ozaki due to the Shobijins' blessing. Ozaki unlocks his true power and defeats the Controller, who triggers the mothership's self-destruct as the group falls back to the Gotengo moments before the mothership explodes. Godzilla and Monster X continue their battle, but Monster X transforms into its true form, Keizer Ghidorah. Godzilla is overpowered by Keizer Ghidorah, but Ozaki transfers some of his own Keizer energy to Godzilla, giving him the strength to destroy Keizer Ghidorah.
Despite the Gotengo's crew proving instrumental in his victory, an enraged Godzilla shoots down the Gotengo before attempting to attack the vessel's crew. Fortunately, Minilla arrives with Kenta and Samon, and convinces Godzilla to spare the crew. Ozaki, Miyuki, Gordon, Anna, and the other humans watch as Godzilla and Minilla return to the ocean.
