Jiro is running with Reiko and Akida from a bunch of machines (sent to capture Akida). When suddenly, a mysterious Kikaider shows up and defeats them. The Kikaider takes the trio to a temple and the reverend there tells Jiro that the Kikaider is known as 01 and Ichiro. Ichiro is the older brother of Jiro but unlike Jiro, he is simple and has no conscience circuit. Ichiro then agrees to go with Jiro so that he can help.

Jiro and Ichiro are having a argument because Ichiro feels that Jiro shouldn't trust Reiko and Akida. He says that little is known about them and they might turn out to be spies or something. Jiro disagrees and says that he trusts Reiko, making Ichiro walk away from them. Ichiro then encounters a girl android named Beijinder and a fight between them breaks out. Jiro shows up and tries to help but his attempts were basically futile. When Beijinder was about to finish Jiro, Reiko shows up and tells Jiro to look out behind him. Jiro turns around punches Beijinder square in the face. Beijinder is so pissed off at Reiko and charges at her but couldn't attack. Something in her was holding her back. Beijinder then leaves. Later that night, four Hakaiders shows up and one of them happens to be Gill. Gill explains that when Jiro destroyed the DARK hideout, almost all his men died. He then transfered his brain into a Hakaider's body so that he could live forever. He then goes on to explain that the three other Hakaiders contains the brains of his most trustworthy men. Gill then demands that he wants his son, Akida, back. The four Hakaiders transform into one huge Hakaider and in order to defeat it, Jiro and Ichiro has to team up. Together, the two brothers defeat the Hakaiders. As Jiro and Ichiro watch the explosion, Ichiro asks Jiro if he really trusts Reiko. Jiro says yes and Ichiro tells him that he trusts them too because he trusts Jiro.

Jiro, Ichiro, Reiko, and Akida are once again being chased by machines sent to capture Akida. They are saved by another Kikaider. This Kikaider is Jiro and Ichiro's younger brother, known as 00 or Rei. As they continue to run, now with Rei by their side, Reiko remembers the place as somewhere she's been before. She tell the three Kikaider brothers that she's been here before and they head down there to check it out. As soon as they got down there, a barrier surrounds the Kikaiders, paralyzing them. Gill then shows up and tells Reiko that she is actually a android created to protect Akida and he was the one that put the memories into her head. Reiko refuses to believe Gill until he makes her transform. As Gill gets ready to kill her, Beijinder transforms into her robotic form and grabs Akida and Reiko. She then breaks the barrier surrounding the Kikaiders and flies off with Akida and Reiko. As the Kikaiders fight more machines, Beijinder and Reiko are flying through the forest. AS Beijinder takes the lead, Reiko drops the 'Pinnochio' book she got from Jiro earlier and heads back with Akida to find it. As she spots the book, she puts Akida down and goes to retrieve it. As soon as the book was in her hand, Gill shows up and shoots her. Akida watches in horror as Reiko falls to the ground. When the Kikaiders show up, they find Reiko's bleeding head and from out of the bushes, a sad looking Beijinder also discovers what's left of Reiko as well.

Ichiro, Jiro, Rei, and Beijinder discover that all four of them, as well as Reiko, are siblings. They are androids created from the same design by Dr. Komyoji. Together, they decide that they should go save Akida and prevent Gill from destroying the world. They head into Tokyo to find a humongous robot built by Gill, called the Armagedon Lord, destroying it. They try and fight the robot but failed miserably. Ichiro, Rei, and Beijinder are captured, leaving Jiro by himself. Jiro finds his way into the robot and find Akida in it's heart. Rei and Ichiro appears and beats Jiro up. Jiro is puzzled at why his brothers are attacking him when he suddenly goes unconscious. When Jiro wakes up, he finds himself in a machine. Gill then comes into the chamber and explains to Jiro that he had installed a submission circuit into each of them (Ichiro, Rei, Beijinder, and himself). Gill then calls Beijinder into the room and turns the submission circuit in Jiro, on. Gill then orders Beijinder to look after Jiro while he destroys the country's capital. Jiro tricks Beijinder into letting him go. Beijinder believes him and he heads out to find Akida only to discover that he's not there. Jiro's next target is Gill. He seeks out Gill and when Gill summons Ichiro and Rei to destroy Jiro, Jiro destroys them both. Gill is shocked at Jiro's behavior. Jiro then explains to Gill that it's the submission circuit that allowing him to lie, destroy his own brothers, and it's going to let him kill a human. He takes Gill by the head and squishes his brain. He says from that day foward, he shall at last become fully human and he really does.

Continuing where Kikaider 01 the Animation left off, Jiro is still wandering the streets trying to fight off any evil inclinations that Gill's submission chip left in him. Upon meeting a local high school boy Jiro attacks him, only to find out that the boy is Inazuman. Inazuman doesn't want to destroy Jiro, but he can't just leave Jiro alone.