A young man named Kazuya Oki volunteers for a radical cybernetic surgery as part of an International Space Development Program in the United States. His goal is to become an astronaut capable of surviving the vacuum of space without a bulky suit, a pioneering cyborg codenamed Super-1. However, before he can begin his space mission, the research base is attacked and destroyed by the Dogma Kingdom, a secret extremist organization seeking world domination. Kazuya is the sole survivor of the massacre.

Returning to Japan, Kazuya discovers that while he possesses the cybernetic body of Super-1, he cannot access his transformation abilities at will because the control console was destroyed in the attack. He seeks out his old martial arts master, Genkai, a master of the Sekishin Shorin Ken style. Through rigorous training, Kazuya learns to bypass the need for external machinery, using his martial arts spirit to initiate the transformation into Kamen Rider Super-1. Determined to avenge the scientists who gave him his powers and protect the Earth, he fights the Dogma Kingdom alongside Genkai, his fellow student Benkei, and his supporter Genjiro Tani.

Super-1 is equipped with advanced technology, most notably the Five Hands system. By summoning different colored hands, he can access a variety of powers: the standard Super Hand, the powerful Power Hand, the Reinetsu Hand which generates heat and cold, the Eleki Hand for electric attacks, and the Radar Hand for scanning environments. He also rides powerful machines, including the V-Machine, a Harley-Davidson that converts into the flight-capable V-Jet.

The first major narrative arc sees Super-1 battling the Dogma Kingdom, led by the ancient Emperor Terror Macro and his subordinate, General Megirl. After a long campaign where Super-1 defeats Megirl (who transforms into the monster Death Buffalo), the Emperor is forced to fight personally. Transforming into the bird-like Kaiser Crow, Terror Macro kills Master Genkai in battle. Enraged and grieving, Super-1 destroys Kaiser Crow with his Super Rider Moon Surface Kick, bringing an end to the Dogma Kingdom.

Almost immediately, a more powerful and chaotic organization rises to take its place: the Jin Dogma. Led by Marshal Demon, this group includes the butterfly-masked Princess Yōkai, the hot-headed Commander Onibi, the scheming Doctor Ghost, and the sorceress Staff Officer Witch. The tone of the series shifts as Jin Dogma unleashes a series of bizarre, often household-themed monsters, such as living refrigerators and umbrellas, forcing Super-1 to adapt to unconventional threats. This period also introduces the Junior Riders, a group of children who assist Super-1, reflecting a shift toward a younger target audience.

In the final episodes, Super-1 defeats the Jin Dogma leaders one by one, culminating in a final battle against Marshal Demon, who transforms into the monstrous Satan Snake. Using the powerful Lightning Sword, Super-1 destroys his last foe. Having defeated both evil organizations and avenged his mentors, Kazuya Oki finally fulfills his original dream. He bids farewell to his friends on Earth and launches into outer space, beginning his long-awaited career as an astronaut exploring the final frontier.