Shinoda is a self employed scientist who makes a living tracking Godzilla’s movements and predicting when he will arrive on land. He forms a reluctant alliance with a reporter, Yuki, who is driven to cover Godzilla to satisfy her boss’ demands. Shinoda is at odds with Katagiri, head of the Crisis Control Intelligence agency, who is determined to defeat Godzilla by whatever means necessary. At the moment, Katagiri’s agency is busy investigating the remains of a UFO that crashed into the ocean during prehistoric times. The UFO begins to reactivate its systems and flies towards Japan. The UFO attacks Godzilla, who retaliates with his atomic ray. The UFO crashes into a nearby lake and Godzilla retreats.

Yuki finds evidence that the UFO is hacking into nearby computer networks, searching for information about Godzilla. The UFO takes off again and settles atop City Tower in Tokyo. From there the UFO is able to hack into every computer in the city in its search for information. Shinoda believes that the aliens piloting the UFO have no corporeal form, and are searching for suitable genetic material with which to construct a body, hence the attraction to Godzilla. Godzilla reappears in Tokyo and marches on the UFO, and another battle ensues. The UFO traps Godzilla underneath a skyscraper and extracts some of his tissues. The UFO attempts to construct a new body, but the attempt goes wrong and the alien takes on a monstrous form instead.

Godzilla emerges from the rubble and battles the UFO and the alien. The UFO is completely destroyed. The alien attempts to swallow Godzilla whole and become a perfect clone. Godzilla thwarts this attempt by emitting a burst of energy that destroys the alien as well. Katagiri is killed when Godzilla approaches his command center. Shinoda and Yuki watch helplessly as Godzilla continues his rampage across Tokyo.