Godzilla is a literal force of nature to Japan. The Godzilla Prediction Network (GPN) functions independently to study the monster and predict its 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 fights 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 Shinjuka. After landing atop Tokyo Opera City Tower, it begins to drain all the files about Godzilla from Tokyo's master computers. As it begins to alter the oxygen content of the surrounding atmosphere, 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 its DNA, which the aliens use to reform themselves outside the space ship as the gigantic Millennian. However, the Millennian is unable to control Godzilla's genetic information in the DNA, and mutates into a horrible monster named Orga. Godzilla recovers and brings down the UFO before fighting Orga, but Orga, having absorbed the regenerative properties in Godzilla's DNA, is highly resistant to injury. Orga retaliates and extracts more of Godzilla's DNA in order to become a perfect clone. Godzilla breaks free and sets Orga aflame, but Orga reemerges and attempts to swallow Godzilla whole. As Orga begins to transform, Godzilla unleashes its atomic breath, vaporizing Orga's entire upper body and killing it. 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 reminisce on how Godzilla was wrought by human ambition, prompting Shinoda to suggest that "Godzilla exists in us", as Godzilla begins rampaging through Tokyo.