In an abandoned prison, a gang of criminals breaks in looking for treasure and stumbles upon a man in chains. They accidentally awaken him, and the android Hakaider reveals himself, slaughtering them all before making a desperate escape on a motorcycle. Nearby, a man cornered by security forces attempts to take his own life, but is stopped and captured by an angelic android named Michael.
Hakaider arrives at Jesus Town, a glossy, pseudo-utopia built on the remains of Jerusalem. With no identification, he is halted at the border by a guard but breaks through the electric barrier regardless. In the city, a group of rebels seizes weapons from the heavily armed security force in a bid to subjugate the government, while Gurjev—the seraphim ruler of Jesus Town—takes notice of the android intruder and orders his security to destroy him. Gurjev explains to Michael, who is now revealed to be his head of security, that Hakaider is actually Michael’s failed predecessor who chose to fight for free will rather than submit to enforced peace. The confrontation between Hakaider and Gurjev’s troops is swift and brutal; the rebels, watching from the outskirts, cheer as Hakaider dispatches the armed officers with ease. Among the rebels, Kaoru recognizes the armored savior from her dreams, the knight who would liberate her from oppression.
When Hakaider is knocked unconscious, Kaoru and Arnie, two surviving rebels, slip away with the others’ help and carry him back to their base. Inside, Kaoru reveals a personal and romantic interest in him, while the group exposes a chilling truth: Jesus Town’s celebrated calm masks a darker truth—the government captures dissenters and lobotomizes them to remove free will, a fate that has already touched Michael’s own captives. They explain their plan to overthrow Gurjev’s regime, but Hakaider remains wary and unconvinced, unsure of the rebels’ true motives.
The security force soon discovers the rebels’ hideout and launches a brutal assault. Most of the rebels are killed in a fierce shootout, and Kaoru, along with Arnie, barely escapes the base in time to witness Hakaider’s apparent demise—killed by a rocket launched by the security officers. Wounded and reeling, Kaoru curses the authorities as Michael arrives just in time to severely wound her. Her scream awakens Hakaider from a trance-like state, and he re-emerges to confront the city’s oppression.
Kaoru wanders the streets, declaring the citizens guilty for Hakaider’s death and their own lingering oppression. Hakaider finds her in the crowd and guides her to a hidden oasis—the last refuge in Jesus Town—where she confesses her feelings as she dies, dreaming of riding off into a sunset with him. Fuelled by Kaoru’s death, Hakaider seizes her charm and returns to the city, plowing into the government building and eradicating the security force with a single, devastating strike. He confronts the townsfolk, asking if they still have free will; when they answer yes, he frees them and turns his attention to Michael.
Michael proclaims the supremacy of order over free will, branding this notion as “justice.” Hakaider answers that, if that is justice, then he will embrace evil. Michael gains the upper hand briefly, but Hakaider, wielding a concealed weapon, decapitates him. Gurjev feigns reason to buy time for Michael’s head to be integrated into a large tank, transforming it into a red-and-blue, asymmetrical form. In this new guise, Michael attacks Hakaider, but the knight of fate subdues him again with another concealed weapon. The two clash once more, and as Gurjev’s hold weakens, Hakaider confronts him with resolve. Gurjev fires a final shot with a revolver that misses, and, in a dramatic turn, Hakaider kills Gurjev with a swift strike that scatters feathers.
With Gurjev dead and Michael’s consciousness fading, Hakaider prepares to ride away on his motorcycle, leaving Jesus Town to its uncertain future. He has faced the tyranny of a supposed utopia and chooses to continue his lone vigil, a force of rebellion against the calculus of control.
