Godzilla 2000

Godzilla is a literal force of nature to Japan. The Godzilla Prediction Network (GPN) functions independently to study the mutant dinosaur 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 fights Godzilla to a standstill, 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), but so has the UFO. It frees itself from the JSDF's attempts to contain it, and heads for Shinjuku. After landing atop 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 rooftop, watching the UFO. Almost in response, the UFO broadcasts its message of invasion and a new empire on earth, and Shinoda reveals that the aliens are after Godzilla's DNA so that they may re-form their bodies.
Godzilla arrives and again battles the UFO. However, he is subdued by the UFO's assault, and it absorbs some of his Organizer G1, growing into a squid-like creature called the Millennian. However, the Millennian is unable to control Godzilla's DNA and further mutates into a horrible monster named Orga. Godzilla recovers and fights Orga, but it eventually gains the upper hand, and drains more of Godzilla's DNA, trying to convert itself into a Godzilla clone. Finally, Orga opens its maw, intending to swallow Godzilla whole, but Godzilla tricks it by shoving his head into its throat willingly. While Orga begins to transform, Godzilla unleashes his nuclear pulse, killing Orga. Godzilla then kills Mitsuo Katagiri, head of CCI, before beginning a rampage through Tokyo.