In a futuristic society, a 15-year-old prostitute named Rune Balot is rescued after being nearly killed. She is subconsciously given the choice to continue living due to an emergency ordinance to preserve life called Mardock Scramble 09. Turned into a cyborg, Balot is then given the choice of assisting the investigations against the man who tried to terminate her. He is part of the powerful October corporation that is stealthily conducting illegal activities.

Rescued from the deadly assault on their headquarters, Rune Balot finds temporary shelter in paradise a high-tech laboratory where the scramble 09 protocol originated

Taking place in a futuristic city called Kamina City, Rune Ballot is a young prostitute who was taken in by the notorious gambler Shell Septinous. One night, Shell abandons Rune and attempts to murder her in an explosion. However, she is rescued and transformed into a cyborg by Dr. Easter. An Artificial intelligence in the form of a Mouse accompanies her to adapt to her new life. Rune is trained to use the advanced technology fitted on her to defend herself against Shell's attempts to have her killed to stop her from testifying against him.