Texhnolyze unfolds in Lux, a dark underground city where people survive in fear and despair under the control of rival criminal factions. Cut off almost entirely from the surface, the gangs depend on mining raffia, the rare substance that gives the city its purpose and supports the cybernetic transplants known as texhnolyze. These implants can replace parts of the human body without triggering an immune response, and the influential Class uses them for research while overseeing Lux's fragile order.
The Class entrusts its executive authority to Organo, led by Keigo Oonishi, a self-righteous man whose own texhnolyzed legs are said to let him hear the voice of the city. That uneasy balance begins to collapse when a mysterious visitor, Kazuho Yoshii, launches a string of crimes that drives the gangs against one another.
As violence spreads, new figures are drawn into the conflict: Ichise, an ex-boxer mutilated by Organo and later texhnolyzed by Eriko "Doc" Kamata; and Ran, a young florist who can see the future. While Lux sinks deeper into madness, Ichise and Ran become central to the greatest crisis the city has ever faced.