A three-way power struggle erupts between the International Police Organization, the secret society known as Big Fire, and the mysterious Murasame Clan, with the fate of the world hanging in the balance. At the center of this conflict is twelve-year-old Daisaku Kusama, a boy who possesses a special wristwatch that allows him to control Giant Robo, the most powerful robot ever constructed. The story takes place in a separate reality from the earlier Giant Robo OVA, exploring the true nature of the GR Project and the enigmatic leader known only as Big Fire.

The narrative begins as Daisaku travels by plane to visit his father overseas. A man attempts to poison him, and a woman named Ginrei, who possesses teleportation abilities, leaps from the aircraft. Daisaku is subsequently picked up by an agent of Big Fire, only to be immediately attacked by the Experts of Justice, the elite task force of the International Police Organization. Soon, all factions learn of an impending doomsday prophecy, and many come to believe that Daisaku himself may somehow trigger the disaster.

Daisaku finds himself caught between the warring organizations, fleeing both Big Fire and the Experts of Justice while desperately trying to prevent the escalating conflict from destroying countless innocent lives. The Bashtarle tragedy, a catastrophic accident that occurred ten years prior during the development of a revolutionary new energy source called the Shizuma Drive, haunts the story and holds the key to understanding the present crisis. Survivors of that incident include Go Gakujin, an expert on Shizuma technology who serves the IPO, and Genya, the son of scientist Dr. Franken von Fogler, who later emerges as a tool of Big Fire consumed by vengeance. Ginrei, Genya's sister and another survivor, possesses powers that allow her to escape danger.

Other key figures include Shizuo Chuujou, the leader of the IPO who wields a devastating power he is cautioned against using. Among the Magnificent Ten of Big Fire stands Alberto, an operative who distrusts his allies and bears a deep hatred for Taisou, a powerful IPO member who once cost him an eye. The Murasame Clan introduces Kenji Murasame, an immortal being whose inability to die becomes his curse as he watches everyone he cares for perish around him.

As the story progresses, Daisaku must learn to control Giant Robo while navigating the conspiracy that links all three factions to the Bashtarle disaster. The series builds toward a revelation of the hidden truth behind the accident that set everything in motion, as the war between the organizations threatens to ignite a catastrophe that could burn the Earth to ashes.