In a near-future Japan, the government initiates the ARK Project, a scientific endeavor led by brilliant robotics engineer Dr. Nobuhiko Kohmyoji to create androids that will serve the public and improve daily life. Dr. Kohmyoji develops two advanced prototypes. His creation is Jiro, an experimental android equipped with a revolutionary Conscience Circuit designed to simulate human emotion and moral judgment. The other is Mari, a combat-oriented android built by Dr. Kohmyoji's rival, Professor Gilbert Kanzaki.

The project takes a dark turn when Dr. Kohmyoji dies under mysterious circumstances. Shortly after his death, his two children, the wary Mitsuko and the young Masaru, become targets of the Japanese Defense Minister, who seeks to seize the late doctor's research. Jiro, following a final directive from his creator, intervenes and vows to protect the children. As they flee, a data chip containing the sum of Dr. Kohmyoji's revolutionary research is revealed to be hidden inside Masaru's body.

The situation escalates when Mari tracks down Jiro and the Kohmyoji siblings. After a confrontation, Mitsuko and Masaru agree to go with her without resistance, leading to the extraction of the data chip from Masaru. With the research in hand, the Defense Minister repurposes the ARK Project into the DARK Project (Developing Advanced Research by Kohmyoji) and forces Professor Kanzaki to complete the work. Jiro is then attacked by a powerful new android, Hakaider. In a shocking revelation, Hakaider is revealed to be Professor Kanzaki himself, who has surgically placed his own brain into a powerful android body to further his ambitions.

In the climactic battle, Hakaider lays waste to the ARK Project facility. As the villain attempts to destroy everything, Jiro chooses to defy his programming, fully exercising his free will to protect the Kohmyoji siblings. Jiro engages Hakaider in a final, destructive fight and manages to defeat him, but at the cost of his own android body. In the aftermath, Mitsuko is left to mourn the heroic android, vowing to one day rebuild him. A post-credits scene reveals that the Defense Minister survived the destruction and, alongside Mari, confirms the official launch of a true, more sinister android project.