Godzilla is a literal force of nature to Japan. The Godzilla Prediction Network (GPN) functions independently to study the monster and predict his landfalls. Meanwhile, the scientists of Crisis Control Intelligence (CCI) find a sixty million year old UFO deep in the Japan Trench. As CCI attempts to raise the UFO to study it, it takes off into the sky on its own. Godzilla arrives and battles the Japan Self Defense Forces, now equipped with powerful Full Metal Missiles, but the UFO appears, searching for genetic information that only Godzilla possesses. It defeats Godzilla, driving the monster underwater, and then lands to replenish its solar power.
Yuji Shinoda, the founder of the GPN, discovers the secret to Godzilla’s regenerative properties (named Organizer G1 in the Japanese version, but Regenerator G1 in the North American release), but so has the UFO. It frees itself from the JSDF’s attempts to contain it, and heads for Shinjuku. After landing atop Tokyo Opera City Tower, it begins to drain all the files about Godzilla from Tokyo’s master computers. CCI attempts to destroy the UFO using explosive charges, but Shinoda, attempting to find out more about the aliens, is nearly caught in the blast. He survives, and joins the rest of the cast on a nearby rooftop, watching the UFO. Almost in response, the UFO broadcasts its message of invasion and creating a new empire on Earth, and Shinoda reveals that the aliens are after the regenerative properties contained inside Godzilla’s DNA so that they may use it to re-form their bodies.
Godzilla arrives and again battles the UFO. However, Godzilla is subdued by the UFO’s assault, and the UFO absorbs some of his DNA, which the aliens use to reform themselves outside the space ship as the gigantic Millennian. However, Earth’s atmosphere is different to the one the Millennian used to live in and so when he exposes himself to the atmosphere, he mutates into a horrible monster named Orga. Godzilla recovers and fights Orga. Godzilla first gains the upper hand, but Orga calls on the UFO, which relentlessly strikes Godzilla down and brings Orga Godzilla’s DNA. Godzilla brings down the UFO, and furiously beats down Orga again, but with Orga now having absorbed Godzilla’s DNA, Orga retaliates and nearly swallows Godzilla as a whole. While Orga begins to transform, Godzilla unleashes his atomic breath, vaporizing Orga’s entire upper body and killing him. Mitsuo Katagiri, head of CCI, dies when Godzilla partially destroys the roof of the building where he, Shinoda and the scientists were observing the battle. The remaining cast on the roof wonders why Godzilla protects them, even though he attacks them and they attack him. They eventually come up with, and agree on, the theory that perhaps “there is a piece of Godzilla in all of us” as Godzilla begins rampaging through Tokyo.