The film is set in a near future chaotic Japan. A mad scientist known as "Key Man" has created a virus that mutates humans into monstrous creatures called "Engineers" that sprout bizarre weapons from any injury. The Tokyo Police Force has been privatized to deal with this new threat of engineers, so a special squad of officers called "Engineer Hunters" are created to deal with them. However, unlike the average police force, the Engineer Hunters are a private quasi-military force that utilizes violence, sadism, and streetside executions to maintain law and order.

Helping the police force is Ruka, an anti-social, self-harming loner, who is very skilled in dispatching the engineers. Along with helping the police, she is looking for the killer of her father, an old-fashioned officer who was murdered in broad daylight by a mysterious assassin. Ruka soon receives a new case to hunt down Key Man. When she meets Key Man, Ruka finds that they both are seeking vengeance against the corrupt officers who killed both of their fathers many years ago. However, in a highly ironic fashion, it was Key Man's father who actually murdered Ruka's father. Soon afterwards, Ruka's life takes on bizarre, tragic twists and turns.