Countries around the world have signed an agreement to reduce military forces to 0.1% of the population and ban the development of weapons of mass destruction. However, this has simply changed the conflict from weapons to intelligence warfare. In Japan, a special spy training agency called the "Church" has been established. These agents, known as Sakura, must follow an iron code and cannot form relationships with anyone other than their assigned "Messiah". This is the cruel fate of Sakura candidate Shiba Shusuke who is tasked with investigating a member of the council.