Former detective Tokisaka Reiji is recruited by a former colleague to investigate a series of gruesome discoveries: severed limbs of young women that surprisingly show signs of life. As Reiji navigates a mysterious request from a girl named Kuchiki Touko to find her "real self" and collaborates with a provocative coroner to link the victims to Ouba Girls' Academy, he finds himself entangled in a disturbing case that mirrors a creepy urban legend.
As the number of missing students from the academy rises, Tokisaka investigates a disturbing link to a writer and artist named Mamiya Shinji. While uncovering secrets about Touko's biological origins, Tokisaka pursues a lead to a secluded studio, only to discover that the suspect has vanished, leaving behind a haunting connection to the legend of the "Girl in the Shell."