A quiet conflict erupts when a global terrorist organization known as G.O.D., the Government of Darkness, approaches a brilliant robotics scientist named Keitaro Jin. They demand he collaborate on their plans for world domination, but Jin refuses. In retaliation, G.O.D. launches a brutal assault on his home, fatally wounding both the scientist and his son, Keisuke Jin, an oceanography student home on break. Before succumbing to his own injuries, Keitaro Jin performs emergency cybernetic surgery on his dying son using his life's work: a prototype改造人間 (kaizō ningen), or modified human, designed for deep-sea exploration. Keisuke survives, reborn not merely as a man, but as the powerful Kaizorg soldier known as Kamen Rider X.

Now a cyborg with the ability to withstand immense ocean pressures and possessing superhuman strength and speed, Keisuke is driven by a need for vengeance and a sense of duty. He wields the Ridol, a versatile multi-form weapon stored in his belt that can extend into a staff, a whip, or a sword. His motorcycle, the Cruiser, is uniquely designed to travel not only on land but also through the air and underwater, perfectly suiting his aquatic combat specialization. As Kamen Rider X, Keisuke begins a solitary crusade against G.O.D., struggling with his new identity as a cyborg and the loss of his human normalcy. He finds an early ally and father figure in Tobei Tachibana, a veteran supporter of previous Kamen Riders who runs a coffee shop and provides him with guidance and a base of operations.

The series unfolds in two major narrative arcs, each defined by a primary antagonist. The first half is dominated by Apollo Geist, the flamboyant and ruthless Chief of Internal Secret Police for G.O.D. He commands a legion of monsters based on figures from Greek and Roman mythology, such as the serpentine Hydra and the sea god Neptune. After a series of intense battles where Keisuke continually proves his worth, Apollo Geist is seemingly destroyed, only to be revived with even greater power. Their conflict reaches its climax in a final, decisive battle that leaves Apollo Geist defeated for good.

Following Apollo Geist's fall, the true mastermind behind G.O.D. emerges: the colossal and terrifying King Dark. This second arc introduces a new wave of bizarre monsters, each a chimera combining an animal with a famous historical or fictional figure, such as Starfish Hitler and Spider Napoleon. King Dark is eventually revealed to be a giant, nearly indestructible robot controlled by the disembodied brain of Dr. Noroi, a former colleague and friend of Keitaro Jin who harbors a deep resentment. In the series' final confrontation, Keisuke must not only destroy the mechanical behemoth King Dark but also come to terms with the tragic legacy of his father's research. As the series concludes, having defeated the leadership of G.O.D. and avenged his father, Keisuke Jin rides off on the Cruiser, his mission complete, but his existence as Kamen Rider X a permanent part of who he has become.