A mad scientist named Mad Oniyama attempts to take over Earth, and wants to use Godzilla as his main pawn. To get the beast, though, he has to deal with two brothers, Hideo Kaneko and his brother and Team G agent Yosuke; their friends; and Godzilla himself. Reviving and altering the DNA of several monsters including Megalon, Biollante, Gigan, and others, he is at one point aided by a version of himself from the 25th century, who uses a time machine in an attempt to alter the past. The manga ends when Godzilla, Oniyama's ultimate creation King Godzilla and Oniyama fall into the crater of a volcano.

A single-chapter story is included at the end of Volume 2, titled Street Fighter Godzilla. In this story, Godzilla, dressed as Ryu from the Street Fighter series, fights Hedorah (who is dressed up to resemble Blanka from the same series) while a Mothra Larva named Mosuko struggles to declare her love for Godzilla.