When Mitsko heads out to the forest to talk to Jiro, a flute that only Jiro could hear, starts playing. Jiro, under the control of the flute, takes Mitsko by the neck and starts choking the life out of her. When the flute stops playing, Jiro realizes what he's doing and drops Mitsko. Mitsko calls Jiro a mad machine and says that she should never have trusted him. Jiro got upset and decided that it'll be best not to stay any longer. So he got on his motorcycle and rode away.

    Mitsko has just hired Detective Hattori to go find Jiro. Hattori begins his search immediately and has heard from people that Jiro appears in front of the puppet clock every hour.

    Jiro is wandering around town and sees a guy with a guitar. The guy asks Jiro to jam with him but Jiro says he's never played before. The guy teaches Jiro what chords and scales are and right afterwards, Jiro plays like a pro. The guy, thinking that Jiro was lying, called him a freak and told him to get lost. Jiro ran off to the power station and there he sees a spider-like machine. The spider and Jiro begin a fight.

    Hattori and Mitsko arrive to see Jiro on top of the power station. Hattori then tries to reach Jiro by running up the stairs to the top. Jiro destroys the spider but the power station is beginning to crumble. He grabs Hattori and flies him down to the ground and runs off. Hattori promises Mitsko he'll find Jiro and bring him home no matter what because Jiro saved his life.

    The episode starts off with Mitsko dreaming that Jiro was killed. She realizes then that she has taken a liking to him. She begins searching for Jiro and found him playing his guitar to a little girl and her cat. When Mitsko begins to talk to Jiro, an ant-like machine shows up and attacks. Jiro transforms to his Kikaider form and fights. A bum who saw Kikaider ran off, scared. Afterwards, the little girl saw Kikaider and called him a monster and told him to get away from her. Jiro, ashamed of the way he looks, ran off again.

Meanwhile, a group of jobless men were hired to blow up the city and it so happens that Toru was one of them. They had to plant bombs around the city and get out of the city as soon as possible if they wanted to live. After planting his share of bombs, Toru went to find Miyuki and warn her. Upon arriving, Toru came face to face with Jiro. Toru asks where Miyuki was and Jiro told him that Miyuki went to work. Toru then told Jiro to tell Miyuki of the bombs and told her to get out of the city. Then, from out of nowhere, a jaguar-like machine jumps out and slashes Toru on his back. After running away, Jiro convinces Toru to get rid of all the bombs because he knew Toru still cared for Miyuki. Toru disarmed all the bombs while Jiro went to fight the jaguar. When Jiro got back, he found Toru in a pool of his own blood.

    Detective Hattori arrives at the Komyoji residence and tells Mitsko that he has found out something about Dr. Komyoji. When they were talking, the lights suddenly blacked out and Hatttori was knocked unconscious and Mitsko is kidnapped in the darkness. The android that captured Mitsko is a vampire-like machine that also contains a conscience circuit. The android then calls up Jiro and tells him that he has Mitsko. Jiro immediately jumps onto his motorcycle and heads to where Mitsko is being held captive.

    After being kidnapped by the vampire-like android, Mitsko finds herself in the house where she lived in years ago. In there, she finds Dr. Komyoji's diary. She discovers why her father built Jiro, why her mother disappeared, and how her step-brother died.

Masaru, Mitsko's younger brother, finds out that his sister has once again left him alone. He decides to go after them. He acquires the address and immediately goes to the train station. He travels to the woods and meets up with Kuya and Kaito. Kuya and Kaito accompanies Masaru to the cabin and they become "friends." Once there, Kikaider and the two androids begin a fight. Kuya and Kaito are destroyed and Masaru is left crying about why Jiro killed his two friends.

    Mitsko and Jiro set out to find her mother. They find her and she reveals that she did work as a spy for Gill.

Jiro, under the control of Saburo's whistle, is destroying the city. Saburo is the human form of a machine built by Gill for the sole purpose of destroying Kikaider. After the whistling stops, Jiro realizes what he's done and runs off to Dr. Komyoji's lab to calm down. Saburo shows up and challenges Jiro to a fight.

    Saburo changes into his robotic form, Hakaider, and fights Jiro. In the process, Saburo shoots off one of Jiro's arms and demands that the fight must be stopped. He says that he doesn't want to fight Jiro when he's handicapped and with that, he rides off. Jiro tries to chase after him but Mitsko holds him back. She tells him what she's found out about the Gemini and that he should let her fix it. Jiro refuses to have his Gemini fixed for fear that he might lose the love he feels for Mitsko.

    Jiro stands bravely against Gill and in the end, the hideout is destroyed in a huge explosion.

    Jiro is running with Reiko and Akida from a bunch of machines. 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.

    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 transferred 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.

    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 'Pinocchio' 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.

    They head into Tokyo to find a humongous robot built by Gill, called the Armageddon 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 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 forward, he shall at last become fully human and he really does.