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. Suspicious of her father's sudden dissapearance, Dr. Komyoji's daughter Mitsuko begins her research for clues. While she's doing that, we meet the Kikaider that the Dr. was working on. He is in human form, and is learning about life with humans. He saves a man from falling off a cliff, he helps two little boys but scares them away.. and then he finds the destroyed laboratory from whence he came. There, he sees the evil robot that blew up the lab, and Mitsuko and her son show up. Mitsuko sees that the Kikaider is the one she was finding clues about, and she tells him how to use his powers. She also tells him that his name is Jiro. Jiro turns into Kikaider form, and eventually destroys the evil robot...

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. In the forest, Jiro and Mitsuko are talking, when all of a sudden a flute plays that only Jiro can hear. He can't stand the music, and it makes him go bad. He starts to choke Mitsuko, and she thinks he's a mad machine. The flute stops playing, and Mitsuko yells at Jiro, causing him to run away..

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. Then, Jiro wanders around and wonders where he should go. It shows Mitsko and her brother, who just woke up, eating breakfast. Jiro then sees a guy playing a guitar and is asked to jam. He then asks if he could be taught how to play, and then after 2 lessons(scales and chords) makes the guitarist yell at him and calls him a freak. Then, two people stand at the puppet clock and see Jiro standing there. The woman calls the girl and tells her Jiro is with them. He then rambles on about how he can't go ""home"" and then runs out of the cafe. He shows up at the clock and then runs off again. He is next seen at a power station, where two police tell Jiro to go home. All ofa sudden, a huge spider drops a web on them and Jiro. The spider calls himself Jiro's brother and starts squeezing the heck outta him. H

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. Jiro changes into a combat form, Kikaider, but also begins to feel ashamed of his ugly apperance. A bum seems him when he changes, and is very scared of the way he looks. Even the little girl who was with Jiro earlier when he was playing his guitar is frightened. In sadness, Jiro flees from Mitsuko once again. While driving home, Mitsuko thinks about the dream she had earlier again, and wondering..""Could Jiro be human?""..

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. 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. Jiro finds Toru by the outside of Miyuki's house, and out of nowhere, Toru is attacked by the yellow jaguar. The android slashes Toru's back, making him bleed. After running away from it, Jiro convinces Toru to shut off all the bombs, because he knows Toru still cares for Miyuki. Later, Jiro finds and confronts the yellow jaguar at the very top of the bridge. He

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. She is kidnapped by the Golden bat, who is an android, and like Kikaider has a conscience chip. Golden Bat calls up Jiro, and tells him that he has Mitsuko. Jiro, immediately, gets on his bike, and rides off to rescue Mitsuko.

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 dissappearance 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 preservedin 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.