Rune Balot is a struggling teenage prostitute in Mardock City, until she meets the ambitious casino manager, Shell, who promises her a better life. Despite feeling indebted to him, Balot can't resist delving into Shell's mysterious past, leading to dire consequences when he tries to kill her. In response to the rampant crime in the city, the authorities introduce the controversial "Scramble 09" law, allowing the police to use any means necessary to revive crime witnesses. After Balot's near-death experience, a professor reconstructs her entire body with synthetic fiber, leaving her struggling to come to terms with her new reality. As she adapts, Balot's desire for vengeance grows stronger as she discovers the shocking truth - Shell is her murderer.