After the incidents involving Heath Oslo, the existence of the Japanese-American counter-terrorist organization, known as CIRS, is now public knowledge. CIRS was rebuilt from the ground up and its more hidden functions were transferred to a new agency: SORD (Social Ops, Research & Development). The main purpose of SORD is to train a new generation of spies to defend the country from future threats. To achieve its ends, the organization has built many schools in the country. Mihama Academy, abandoned after its sudden closure, has become a specialized training school. So, this new Mihama Academy is home to different groups of students who every day work hard to improve their skills. These students put their own safety at risk by immersing themselves in various extrajudicial missions, all for the good of the country.

Mihama Academy—on the surface, a closed learning environment established to nurture students who find themselves at odds with the world around them; in actuality, an orchard-cum-prison built to preserve fruit that has fallen too far from its tree. Yet with the arrival of the institute's first male student, the nearly preposterously opaque Kazami Yuuji, the students at Mihama begin to fall out of step with their predetermined rhythms. Will Yuuji prove to be the element the girls around him needed to take hold of their lives once more, or will the weight of their pasts prove too steep a wall to overcome?