A young boy named Daisaku Kusama finds himself at the center of a global conflict when he becomes the sole person capable of commanding a colossal, atomic-powered robot. The story begins when an ocean liner is attacked by a giant sea monster, leaving Daisaku and a young man named Juro Minami shipwrecked on a mysterious island. They soon discover the island is a secret base for Big Fire, a terrorist organization led by the alien Emperor Guillotine, who seeks to conquer the Earth. Inside the base, a captive scientist, Dr. Guardian, has been forced to construct a massive humanoid robot. As Daisaku and Juro attempt to escape, Dr. Guardian gives the boy a wristwatch-like device, explaining that the robot will obey the first voice it hears. The scientist sacrifices himself in an explosion that activates the robot, and Daisaku's voice becomes its command.

The giant robot, known as Giant Robo, is a towering, pharaoh-like machine equipped with a jet pack and finger-mounted missiles. Rescued by Juro, who is secretly Agent U3 of the international peacekeeping organization Unicorn, Daisaku is invited to join as Agent U7. Together with Unicorn's Japanese branch chief, Commander Azuma, they form the front line of defense against Big Fire. Emperor Guillotine, a tentacled alien who commands from a hidden spaceship at the bottom of the ocean, dispatches a series of monstrous agents to do his bidding. These threats include kaiju such as the tentacled sea monster Dracolon, the rolling metal globe Glober, the alien plant Satan Rose, and the lizard-like Ligon-Tyrox. Daisaku and Juro travel across the globe to counter these attacks, with Giant Robo summoned by the boy's voice to engage the giant monsters in battle, often destroying them with its powerful missiles.

The narrative follows a largely episodic, monster-of-the-week format, with recurring Big Fire commanders like the silver-skinned Dr. Over, the card-themed Black Dia, and the alien Red Cobra carrying out Guillotine's schemes. These plots range from kidnapping scientists and holding cities hostage to stealing advanced technology and manipulating world powers into war. Unicorn agents often find themselves captured or in peril, requiring Daisaku and Juro to infiltrate enemy bases. A notable arc involves the frequent attempts by Big Fire to either destroy or recapture Giant Robo, with their own giant robots, such as GR-2 and GR-3, being deployed to challenge it. Throughout these adventures, Daisaku's courage and resourcefulness are tested, but the bond between the boy and his robot remains the key to victory.

The series concludes with a direct confrontation between Emperor Guillotine and Giant Robo. Having grown to a colossal size himself, Guillotine reveals his body is composed of atomic energy and warns that any attack on him will trigger an explosion large enough to destroy the Earth. As the world faces the threat of surrender, Giant Robo, acting against Daisaku's frantic commands, seizes the emperor and flies into outer space. Guillotine detonates, creating a massive explosion that consumes both himself and the robot. The Earth is saved, but at the cost of its greatest protector, leaving Daisaku and Unicorn to mourn the loss of Giant Robo, which was more than a machine to them.