Deep in the mountains, Dr. Komyoji was about to complete his long time dream in his laboratory when mysterious robot attacks and destroys his lab. Behind the plot is Professor Gil, the evil leader of DARK, an underground organization.

In her search of her father, Mitsuko invites Jiro, the humainoid robot created by Dr. Komyoji, to her but finds out that Jiro has no memory. As she continues her research through data left by her father, she learns that Jiro has a conscience circuit called ""Gemini"" that is equivalent to the soul of a human being.

Jiro stops to look at a puppet clock and hears a boy talk about puppets and remembers Mitsko telling him he's a mad machine. Next, a figure climbs up at a train station and wrecks the train.

Mitsuko has vivid dream of Jiro being killed and realizes she's starting to like him. After searching she finally finds Jiro through the sorrowful sound of his guitar. However, another robot sent by Dr. Gill suddenly appears.

Suspect of destroying the radar tower, Jiro is now on the run from the police. As he wanders around the city, he meets a young woman named Miyuki who tells him that he reminds her of Toru, the man she loves. Meanwhile, Proffesor Gill hires a group of jobless men to blow up the city, one of whom happens to be Toru.

Mitsuko is worried sick about Jiro when Hattori pays a surprise visit to the Komyoji residence. He says he obtained an amazing piece of information concerning Dr. Komyoji. However, suddenly the lights off and Mitsuko is kidnapped in the darkness.

Realizing she's trapped in the same house where she used to live with her mother, Mitsuko's bitter memories suddenly return. She finds her father's diary, which spells out all the mysteries and truths behind her mother's disappearance and the death of her step brother, Ichiro.

The genius robotics professor Dr. Komyoji has created Kikaider, a humanoid robot gifted with a "conscience circuit" enabling Kikaider to simulate real emotions and distinguish between right and wrong. "Jiro", as he is called by Dr. Komyoji's children Mitsuko and Masaru, finds himself struggling to protect Mitsuko and Masaru from the evil Dr. Gill and his androids, and also to understand his own conflicted emotions. Is the conscience circuit a blessing or a curse?

After being told her father is still alive, Mitsuko sets out on a journey with Jiro to find her mother, who knows the whereabouts of Professor Gill. Meanwhile, feeling left out, Masaru sneaks out of Hattori's office and goes looking for Mitsuko and Jiro.

Jiro, Mitsuko and Masaru are still looking for some clue to find Dr. Kimyoji when they accidently run into Chigusa. Conflicting emotoins of love and anger hits both Mitsuko and Masaru, especially when their mother reveals she worked as a spy for Professor Gill.

With the blue print Conscience Circuit found from Jiro's guitar, Mitsuko learns Gemini has the ability to evolve on its own. On the other hand, Jiro, controlled by Saburo's evil whistles, start destroying the city. Not knowing how to control himself, Jiro wanders to the old research lab of Dr. Kimyoji desperately seeking salvation, but Saburo appears once again.

Amazingly, Dr. Kimyoji's brain has been transplanted into Saburo's head while his body is being preserved in the DARK lab. After getting one of his arms destroyed by Hakaider, Jiro allows Mitsuko to fix it from this, their feelings for each other deepen even more. However, afraid of losing his feelings for Mitsuko, he refuses to have his Gemini repaired.

After taking over Hakaider mind, Dr. Kimyoji helps Jiro infiltrate into the DARK hideout. Jiro searches for Gill, who tries to confuse Jiro with his flute, but Jiro's Gemini has grown so close to a human soul that the sound has no effect. To save himself and those he cares for, Jiro bravely stands against Gill to destroy evil once and for all.

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.