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In the underground city of Lux, Ichise is a prize fighter. He angers his promoter, who cuts off his arm and leg. Doc, a former citizen of the sealed city of the Class, is Lux's most talented researcher of Texhnolyze, an advanced prosthetic limb technology. She gives Ichise Texhnolyzed limbs without his consent. Texhnolyze uses Raffia, a substance derived from dead bodies that is harvested in mines around the city's Obelisk. Raffia prevents the user's body from rejecting the Texhnolyze.
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Ran, the current Seer of Gabe, sells flowers in Lux. She can see an individual's possible future. Her followers in Gabe unquestioningly accept her predictions even at the cost of their lives. Gabe is home to the former leaders of Lux, who were overthrown by the Organo. Onishi is the current leader of the Organo and is credited with the current peace in Lux.
Yoshii comes to Lux from the legendary surface. Fed up with the unchanging nature life on surface, Yoshii covertly throws Lux into chaos, pitting the Organo, the Salvation Union, and the Racan against each other. The tensions eventually escalate into a battle in the streets between the three factions. Afterward, Yoshii attempts to convince Shinji, leader of the Racan, to assassinate a Class leader. Onishi arrives to prevent the assassination, and Yoshii almost kills Onishi, but Ichise arrives and kills Yoshii.
Doc goes to the entrance of the Class enclave and attempts to convince their leader, Kano, to take her in and use her Texhnolyze expertise, presenting Ichise as an example that Texhnolyzation can create perfect humans. However, Kano has a different form of Texhnolyzation in mind, so he destroys Doc's research and tries to kill her.
Kano undermines the three factions of Lux and creates an army of Shapes: humans whose entire bodies have been replaced with Texhnolyze, with only their heads remaining intact. The Shapes march on the city and many of Onishi's remaining allies are killed.
Onishi sends Doc and Ichise to the surface to warn of Kano's impending invasion. They discover that the world above is sparsely populated, and the remaining citizens have resigned themselves to extinction and became ghosts. The government is apathetic to the news of the invasion. Doc and Ichise find an old-style movie theater where they see a film that explains that Lux was created when the Class rounded up people who were thought to be imperfect or impure of thought, killing many and forcing the rest into the underground city. Doc commits suicide after seeing what the surface has become. Ichise returns to Lux, learning that the Shapes have captured Ran.
The Shapes begin to stop functioning, and Shinji is killed after killing most of the members of the Class in their fortress.
Ran shows her visions to the people of Lux, driving them mad. She is captured and taken to Kano's sanctum. Onishi goes to the Obelisk, begging the city for guidance. The city, in Ran's voice, tells Onishi to kill the city for driving everyone insane. He chooses to destroy everything rather than living on with madness in body and soul. He stabs the Obelisk, and it bleeds. The crazed men of the city shoot Onishi until nothing is left but his Texhnolyzed legs.
All of the Shapes, as well as Kano, have been rooted to the ground and permanently immobilized. Ichise finds Kano in the opera house. Kano says that he failed in his attempt to use Texhnolyzation to get people to evolve out of their violent ways, and now humanity's self-preserving bloodline has returned to its roots.
Ichise sees that Ran is behind Kano and has been turned into a Shape, but Kano says that she turned her mind off by her own will. Seeing Ichise's rage, Kano says that if Ichise kills him, the one sane man in the city, Ichise will only be embracing his own madness. Ichise responds by punching Kano's head off.
Ichise drops Ran's remains into the pool of Raffia. He leans against a column, watching a projection of a simplistic rendering of one of Ran's flowers. Eventually he slumps over and smiles as he and the city fade away.
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