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.