A mad scientist named Mad Oniyama seeks to conquer the Earth, with Godzilla as his ultimate pawn. To secure the monster, Oniyama must contend with the Kaneko brothers: Hideo and Yosuke, an agent of the monster defense organization Team G, alongside their friends. The story is set after the events of the 1992 film Godzilla vs. Mothra, depicting a world where humanity struggles to survive amidst a surge of giant monster activity orchestrated by a single brilliant but insane mind.

The central conflict revolves around Oniyama’s plan to revive and genetically alter the DNA of numerous classic kaiju to serve his will. Godzilla, awakening from his previous battles, becomes the primary obstacle to this scheme. The narrative is driven by the escalating war between the independent King of the Monsters and Oniyama’s growing army of controlled creatures. This version of Godzilla is portrayed as a prideful and immensely powerful force of nature who believes himself unbeatable, though he shows a begrudging respect for the human G-Team members who aid him.

As Godzilla carves a path of destruction, he faces a relentless series of enhanced enemies. The first is Sea Baragon, a hybrid created from the original Baragon’s corpse spliced with walrus and narwhal DNA. He then battles Neo Biollante and Megalon, who accidentally destroys his own ally. Later confrontations include Mechagodzilla III and Mechani-Kong II, who double-team the monster, and a flying version of Ebirah. The battle escalates with the arrivals of Rodan, a new Anguirus species called Anuirus, a refurbished Gigan, and King Ghidorah III, who possesses the new ability to turn invisible.

One of the most notable narrative arcs involves a version of Mad Oniyama from the 25th century, who uses a time machine to aid his past self in altering history to ensure victory. This science fiction twist raises the stakes, suggesting the conflict spans across time itself. The human protagonists, Team G, work to counter the scientist’s schemes, intervening in monster battles and freeing Godzilla from mind control at a critical moment when Oniyama temporarily bends him to his will.

The manga builds towards a climactic confrontation with Oniyama’s ultimate creation: King Godzilla. This abomination is a genetic chimera combining the body of Godzilla with the heads and legs of King Ghidorah, the wings and brain of Battra, and the concealed head of Biollante, which fires a powerful chest beam. The G-Team deploys their own mecha, Machine G, to assist a weakened Godzilla. In a brutal final battle, the mortally wounded Godzilla manages to grab King Godzilla and hurl himself and the clone into an active volcanic crater, with the evil Doctor Oniyama falling in as well, seemingly ending the threat.

In a unique stylistic choice for a Godzilla story, the kaiju themselves are depicted as having conversations with each other, though human characters cannot understand them. This adds a layer of characterization to the monsters’ brutal and bloody battles, which often feature graphic injuries and dramatic violence. The manga also includes a whimsical bonus chapter titled Street Fighter Godzilla, where Godzilla, dressed as Ryu, fights a Hedorah dressed as Blanka while a lovesick Mothra larva named Mosuko pines for him.