Humans have created an underground realm where the descendants of a rejected past vie for power in the dilapidated city of Lux. Ichise, a former orphan fighter, loses his arm and leg in a brutal attack by a vengeful promoter. Close to death, a young female doctor saves him by using him as a test subject for the latest generation of Texhnolyze prosthetics. Oonishi, a strong leader of Organ, a group that exerts influence over Lux, takes Ichise under his wing, and he becomes increasingly enmeshed in the battle for city dominance. Ran, a young girl prophet, guides him from the shadows throughout his darkest hours. With escalating conflict, Ichise must expose the truth about Lux and fight for survival while accepting his predestined destiny.