Rune Balot lives as a destitute teenage sex worker in Mardock City. One day, an enterprising casino director named Shell picks her up and showers her with everything she could wish for. Embraced by a fabricated purity, an invented history, and the false existence Shell has constructed for her, Balot feels indebted. Yet she remains intrigued by his generosity and begins to investigate his background on a computer. Her inquiry proves disastrous, altering her fate dramatically. When Shell discovers her probing, he tries to kill her by detonating her vehicle.
Because Mardock"s crime rate remains alarmingly high, a new statute known as "Scramble 09" grants police the authority to employ extreme and otherwise unlawful tactics to rescue crime witnesses. Accordingly, they permit a scientist to resurrect Balot from the brink of death by reconstructing her body with reinforced synthetic fibers. Upon regaining consciousness, her bewildered mind shifts toward vengeance as Shell is exposed as the murderer.