A plane crash in the Amazon rainforest leaves a young Japanese boy named Daisuke Yamamoto the sole survivor. He is found and adopted by a local Incan tribe who name him Amazon, and he grows into a feral child living off the harsh jungle. Years later, the Ten-Faced Demon Gorgos, leader of the evil organization Gedon, massacres the tribe while searching for the powerful GiGi Armlet. The tribe's elder, Bago, performs an ancient Incan ritual that fuses the armlet to Daisuke, transforming him into the super-powered warrior Kamen Rider Amazon before dying. Daisuke then travels to Japan, where he is pursued by Gedon, who wants the GiGi Armlet for its world-conquering power.

Unable to speak coherent Japanese due to his wild upbringing, Daisuke is befriended by a young boy named Masahiko Okamura and his sister Ritsuko. Their uncle, Professor Kousaka, is killed by Gedon for knowing their secrets. Daisuke is soon aided by Tobei Tachibana, an old ally of previous Kamen Riders who helps him adjust to civilization and maintain his motorcycle. Initially speaking in grunts and simple words, Daisuke learns Japanese from Masahiko as they fight side-by-side. He is known for his wild, animalistic fighting style, often biting enemies, and his transformation is triggered by a pose rather than a vocal command.

The first major narrative arc focuses on the fight against Gedon. Their leader, Gorgos, possesses the matching GaGa Armlet and rides a massive stone body covered in faces. The conflict culminates in a final battle where Amazon destroys Gorgos, but the GaGa Armlet is immediately stolen by the agents of a new, more powerful enemy: the Garanda Empire. Garanda is revealed to have been the true power behind Gedon, and they launch a series of terrorist attacks on Tokyo to establish their dominion. Their mysterious ruler, known as Emperor Zero, is a powerful being who can negate the GiGi Armlet's abilities.

Notable throughout the series is the tragic character of the Mole Beastman. Originally a monster sent to kill Daisuke, he is exiled and left to die by his own masters after failing. Daisuke rescues him out of pity, and the confused creature becomes a loyal, if unusual, ally. The Mole Beastman helps gather intelligence and protect civilians, ultimately sacrificing his life to help Amazon create an antidote for a deadly mold weapon, proving that even a monster can possess courage and loyalty. The series concludes with Amazon confronting Emperor Zero, fusing the GiGi and GaGa armlets to gain the power needed to destroy the Garanda Empire for good. Having avenged his adopted family and protected his new home, Daisuke Yamamoto returns to the Amazon jungle where he was raised.