An astronaut named Takegami returns to Japan, although he has been, unknowingly, infected by a new virus during his travels. Over time, the man realizes that his body is starting to go through startling changes, and decides to flee before his daughter might make the same discovery. Shortly after leaving, reports start to pour in of an unknown creature seen residing in the Mt. Fuji area that is simply dubbed "M". However, the sightings are dwarfed by the discovery of an advancing Godzilla on the sea floor, not far from the coast of Japan. The Japanese military, part of the Republic of Japan, quickly deploys its forces in an attempt to keep it from coming ashore, but are too late. Fortunately, after the nuclear leviathan destroys a fleet of helicopters, Godzilla disappears underground.

Meanwhile, near Mt. Fuji the astronaut's daughter searches for the mysterious new creature in the area, on a hunch that it might be connected with the disappearance of her father. She discovers the beast, who acts kindly toward her. After spending time with it, she eventually realizes that this creature is, in fact, her father.

Not too much later, Godzilla reemerges from the Earth through a subway system. The astronaut monster M rushes to the scene and attacks Godzilla full on. While this is happening, the astronaut's daughter approaches the Japanese military and warns them that the new creature is her father. The military scoff at the notion, and quickly attack both creatures. The space monster then becomes quickly out matched by Godzilla, and is wounded badly during the confrontation. The beast then abruptly retreats back to the Fuji forest, leaving Godzilla to destroy Japan.

His daughter manages to find the injured monster, and comforts him. The Japanese military meanwhile are attacking Godzilla to no avail as there forces are easily destroyed by the creature. Still wishing to protect his country, the wounded space creature arrives to fight off Godzilla a second time. Unfortunately, the creature is easily crushed by nuclear menace, prompting his daughter to give her life force to her father. The act rejuvenates the extraterrestrial being, and causes the beast to surge with power as it attacks Godzilla again. This time, the creature is able to defeat the nuclear leviathan, and manages to grab the body and carry it off to sea, where they both disappear.

After being awarded the chance to direct the next Godzilla film following the completion of Pyrokinesis (2000), Shusuke Kaneko began quickly working on concepts to base his production around. His first idea was Godzilla vs. Kamacuras, a movie in which Godzilla faced off with the Kamacuras from Son of Godzilla (1967). Kaneko was eager to breath life into the mantis design through heavy CGI work. After learning the insect Meganulon was the basis of Godzilla vs. Megaguirus (2000), though, the director quickly pivoted to search for something more original.

This led to Kaneko's first fleshed out story for his 2001 Godzilla film, in which Godzilla does battle with an astronaut turned uchujin (space alien) dubbed "M". Kaneko worked on a couple of drafts for the idea, the last one he created made full use of the Millennium concept with an alternate reality where Japan had become the "Republic of Japan" with a large military at its disposal rather than a Self Defense Force. However, Kaneko finally dropped the idea, feeling the story was too depressing for the type of movie he wanted to make, and instead began work on a more lavish concept: Godzilla X Varan, Baragon and Anguirus: Giant Monsters All-Out Attack.

Note: The project was untitled when it was dropped. The concept for the monster above was created by artist Raf Gonzalez for use by Toho Kingdom. It was not created by Toho nor is it their official look for the unused character.