Not everyone is as docile as they seem; some have the natural ability to kill without remorse or difficulty. These cold-blooded killers are known as "Innocent Devils," people who kill instinctively.

Innocent Devil follows the petite Touko Kamijou, a talented criminal psychologist, who sees the Devils as the next step forward in human evolution. She works alongside the young Akane Shinkai, a girl who lost both her parents to a Devil eight years ago. Akane and Touko research the Devils so that, one day, Akane may truly understand the emotions associated with killing another human being.