A typical high school student Ryo Takatsuki discovers that his right hand, which was injured in an accident years earlier, was implanted with 'nano-machines', microscopic robots that turn it into an 'ARMS', a powerful metamorphic weapon. Hayato and Tomoe, two transfer students at his school, possess similarly lethal mechanical appendages. All three students are attacked by assassins sent by the mysterious organization 'Egrigori' which wants to claim them for itself.