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. Written by ANN

Motoko and Batou work to try to stop a terrorist organization whose symbol is the Scylla. Meanwhile, Togusa investigates a murder of a man who possessed a prosthetic leg manufactured by the Mermaid's Leg corporation.

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

Third film of the Mardock Scramble series. Rune Balot goes to a casino connected to the October corporation to try to wrap up her case once and for all.