An invading alien force known as the Dark Horror Army, led by the robotic emperor Great Darius, launches an assault on Earth. Their home planet of Zela is being consumed by a black hole caused by their dying sun, Sigma, and they seek to conquer Earth as their new world. The aliens utilize their advanced technology to create artificial black holes, causing catastrophic phenomena such as strange formations under the Bermuda Sea and inexplicable ice-free zones in Antarctica.

In response to this threat, the brilliant Dr. Daimonji (also known as Professor Hi-Tech) constructs the Daiku Maryu, a gigantic, semi-transformable dragon-shaped carrier ship. This vessel is the first of its kind in super robot fiction to serve as a mobile carrier for a giant robot. The ship's head and torso detach to form the core of the titular super robot, Gaiking, which combines with limb units launched from the carrier to become a humanoid fighting machine distinguished by its skull-shaped golden chest and horns.

The mecha is piloted by Sanshiro Tsuwabuki, a former star baseball player whose career was ended when his throwing arm was injured in an attack by alien agents. He is recruited for this role because his latent, powerful psychic abilities make him uniquely capable of controlling Gaiking, as all other potential candidates with similar powers have already been assassinated by the invaders. Sanshiro joins the Daiku Maryu's diverse crew, which includes other skilled individuals such as an American navy pilot, a sumo wrestler, and a kickboxing champion, all of whom operate the carrier and its auxiliary support machines. These support vehicles include the plesiosaur-like Nesser for water, the pterodactyl-like Skylar for air, and the triceratops-like Bazolar for land operations.

Throughout the 44-episode series, the crew travels to real-world locations as they battle the forces of Great Darius and his four lieutenants, the Death Cross Generals. The narrative reveals deeper lore, explaining that the people of Zela had secretly visited Earth millions of years prior, influencing its development and hiding monsters across the planet. The conflict follows a classic monster-of-the-week formula where the Dark Horror Army unleashes a new beast, forcing Sanshiro to launch Gaiking from the Daiku Maryu to engage in combat, often culminating in the use of Gaiking's powerful finishing attack, the Hydro Blazer.