In the dark underground city of Lux, people live in fear and despair under the rule of various criminal factions. Almost secluded from the surface, the gangs' only interaction with the outer world is their mining operation of "raffia," which is the raison d'être of the city.

Available only in Lux, this rare substance is the basis of "texhnolyze" transplants that permit humans to replace parts of their body with cybernetic prostheses. The latter have the particularity not to trigger an immune response in their hosts and the "Class" has the privilege to conduct research on them. This elusive organization, also in charge of the raffia production, delegates its executive authority to a group called Organo led by Keigo Oonishi—a self-righteous man with texhnolyzed legs who is rumored to hear the "voice of the city."

The fragile balance of powers in Lux is disturbed when a mysterious visitor named Kazuho Yoshii begins committing a series of crimes that puts the gangs at each other's throats. In the midst of the chaos, new actors emerge: Ichise, an ex-boxer mutilated by Organo and recently texhnolyzed by Eriko "Doc" Kamata; and Ran, a young florist who can see the future. While Lux steadily plunges into insanity, both Ichise and Ran find themselves involved in the greatest crisis the city has ever faced.