Three years after the android Kikaider destroyed the criminal organization DARK, the evil Professor Gill resurfaces. Having survived by transplanting his brain into the powerful robotic body of Hakaider, Gill assembles a new Hakaider Squad consisting of Red Hakaider, Blue Hakaider, and Silver Hakaider. Their goal is world domination, and the key to their success lies with a young boy named Akira, who carries a mysterious secret literally etched onto his body. Sensing the resurgence of evil, the circuits of a powerful new android awaken from a long slumber within a Niou statue. This is Ichiro, also known as Kikaider 01, a solar-powered warrior who serves as the older "brother" to the original hero, Jiro (Kikaider). Unlike the conflicted Jiro, Ichiro is a confident and straightforward fighting machine sworn to protect Akira.

As Ichiro battles the Hakaider Squad, he is joined by Jiro, who has survived his previous ordeals. Together, they defend Akira and his guardian, Rieko, from the villains who seek to unlock the blueprints for a devastating giant robot hidden on the boy's back. The Hakaider Squad utilizes various schemes and transforms into monstrous forms like the Blue Crocodile and Red Centipede before being destroyed by the combined efforts of the two android brothers. However, their victory is short-lived as a larger, more mysterious organization called SHADOW emerges, led by the enigmatic Big Shadow. The powerful Shadow Knight becomes a new adversary, and Professor Gill is reluctantly absorbed into this new hierarchy as a high-ranking member, continuing his quest to build the ultimate weapon. The conflict escalates when it is revealed that Professor Gill has a second son, Hiroshi, who holds the other half of the robot's blueprints on his back.

As the series progresses, the narrative deepens with the introduction of new allies and rivals. Due to Jiro’s actor having scheduling conflicts, a new heroine named Mari appears. She is revealed to be Bijinder, a female android initially created by SHADOW to destroy Kikaider 01. However, she struggles with her programming and ultimately betrays her creators to become a trusted ally of Ichiro and Jiro, adding a complex layer of loyalty and identity to the android cast. The heroes also encounter the wandering samurai robot Waruder, who is torn between his mission to kill 01 and his developing feelings for Bijinder. The fight against SHADOW takes the heroes across various fronts, eventually revealing that the organization has a base on the moon and commands an army of Deathbot commanders. The central narrative arc revolves around the race to secure Akira and Hiroshi to build the Armageddon Android, a giant devil robot of immense power, leading to a final confrontation where the three Kikaider units must unite to prevent global catastrophe.