Hayato Shingu must confront the horrors of his past as he, Ryo, and Takeshi return to his village which was destroyed by Egrigori ten years ago. Egrigori has subsequently turned the place into a research lab dealing in nanotechnology and human experimentation. But before they can find out any more, the Arms kids must survive a battle against The Crimson Triad, a high-tech super-agent group known for their ruthless bloodlust.