An astronaut 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.

However, the sightings are dwarfed by the discovery of an advancing Godzilla on the sea floor, not far from the coast of Japan. The JSDF 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 rushes to the scene and attacks Godzilla full on. While this is happening, the astronaut's daughter approaches the JSDF and warns them that the new creature is her father. The JSDF scoff at the notion, and quickly attack both creatures. The space monster then becomes quickly outmatched 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 JSDF 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.

This was Shusuke Kaneko's original story for his 2001 Godzilla film, after being given the project by Toho. However, Kaneko dropped the idea, and instead began work on a more lavish concept that included Anguirus, Baragon and Varan as Godzilla's opponents.

Note: The project was untitled when it was dropped, and Godzilla's rival in the film was never named. The word Uchujin, substituted here for the title and the creature, is merely "space alien" in Japanese/Romaji. Also, no picture or concept art exists for the creature, and the above design was Toho Kingdom's interpretation of the monster.