Ichise is currently living his life as a fighter in an underground fighting ring. He is incredibly strong and is rewarded for his efforts with a nice whore. She goes kind of crazy and he throws her off during their 'love making'. As a result, her 'employer', Aida, calls up a member of Organ, Isshii, to punish Ichise. Isshii cuts off Ichise's right arm. At the same time, we see our first sighting of Yoshii, a member of the Class who has come down to Lux for reasons unknown at this point. When he gets to the bottom of the stairs that connect the two worlds, he meets Ran, a girl from the nearby village of Gabe, which is situated on the outskits of Lux. Ran leads him to the Elder of Gabe where they are soon accosted by a couple members of the Alliance. Yoshii protects Ran and the Elder and fights them off. We are also introduced to Oonishi, the leader of Organ.
Things just aren't going Ichise's way. In an attempt at blind rage, he gets his left leg cut off by Isshii (in addition to his right arm in the first episode). Oonishi sees his men at the warehouse and scolds Aida for not coming to him first. He then tells Ichise that he won't kill him because he still has the will to live. After this, Ichise drags himself through the streets with his severed limbs tied to his good leg. He eventually fashions a makeshift crutch, but it doesn't help him that much. Yoshii and the Elder have a little chat. Yoshii says that he didn't come down for any particular reason. The Elder doesn't really know if Yoshii's coming is a good or a bad omen. He has Yoshii take the train to Lux with Ran. On the train, we learn that Ran comes to the city alone often and that she sells flowers at the market there. We also learn from the Elder that she has the ability to see into the near future. Oonishi realizes that his men are getting restless because of the assassination
We see some flashbacks of Ichise's childhood. His father was tortured and hanged for some crime he committed. A short time later, his mother became very ill and died. He received a vial from the hospital that contained some of her cells and he had kept it with him since. He wakes up in Doc's Lab and he freaks out that he doesn't have the vial. She tells him that she used the contents as part of a new Texhnolyze Unit that will become his new arm and leg. He freaks out, but she knocks him unconscious. Some men from the Alliance attempt to assassinate Oonishi, but fail miserably. We learn that Kimata, the Alliance's leader, is Texhnolyzed, which is strictly against their ideals. We also see Oonishi's wife, Mana, for the first time. She is very unresponsive and almost seems to be off in her 'own world'.
Yoshii explains the politics behind Lux: At one time it was ruled by the Elder of Gabe, but in recent times the power has switched to Organ because of their military strength and efficient organization. He says that the people of Lux have lost their 'natural healing process' in their bodies. He also says that the Class built their own world to live in isolation from the people of Lux. Doc explains all about the Texhnolyze process. Basically, is connects to the body's nervous system and transmits its own 'neural information' to the brain (hence why people with Texhnolyze have crazy vision). She also explains that the reason it all works is because of Lafia, which is mined in the Mine. Lafia basically relaxes the body's instinct to reject organs that are alien to the body and allows Texhnolyze to sync with the body.
Ichise continues to struggle to adapt to his new Texhnolozyed body, what horrors lay a head. Yoshi, a mysterious visitor from the surface is gathering information concerning the gangs of Lukuss, what are his plans?
Ichise finally confronts the man responsible for severing his limbs. After applying a Repetition of punches, he is retaken by the Organo.
With tension building between the Union and the Organo, will a war between gangs occur? What is Yoshii planning, is he the one responsible for tension between the gangs? Shinji has big plans for Lukuss, where does Ichise fit into his plans?
It now appears an all out war between rival gangs is looming, who will survive the conflicts and who will be crushed?
Blood has been spilt on to the streets of Lukuss, all because of the work of Yoshii, what does he hope to gain by all of this bloodshed? Onishi is losing his grip of power to those around him, how much longer can he remain in control.
The war for power continues, and Yoshii is helping to keep the hatred between the powers alive and well. A top official of the Organo has come down from the hil, what if anything, will any of the warring factions do about this sudden appearance.
Those who want to take control, must now hold their ambitions in check. Onishi is now under the protection of the higher ups in the organization, but there are those who continue to move against him. Their ambitions might lead them to their downfall.
Ran is overwhelmed by a vision of Ichise's future.
Gabe acquires high-quality weapons, beyond even those that the Alliance or Lakan could own and are preparing for a revolution.
Ichise and Doc meet with Class.
Michiko talks to Shinji behind Onishi's back. Kohakura orders Ichise to kill Tsujinaka.
Ran is being discussed as a Watcher, relieving the duties her grandfather. The invasion of Shapes has reached the city of Lakan. A group of Salvation Alliance members discover someone is Texhnolyzed.
Shapes continue the rampage as it targets Onishi, Michiko, and Ichise. Doc reveals to Ichise what really happened to the vail containing her mother's long-dead cells.
Ran has a vision of the Obelisk sweeping over her. The killings, mostly against the Organo continue. Shinji and Onishi meet with the elders of Class.
Doc and Ichise arrive at the surface world. They then meet a little ""girl"" Saginuma who begins giving them information about the surface world and a history of Lux.
Ichise meets his father's ghost. After trying to re-gain entry to the Lux, Toyama tells Ichise Ran has been captured by Kano for his purposes, then challenges Ichise to a duel.
Voices are creeping the underground world (the film which Doc and Ichise watched) retelling Lux's history, the surface world of Hades, and many prophetic things about Ichise. Shinji attemps to kill everyone of the Class. A voice sounding like Ran tells Onishi to kill the Obelisk.