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. Whatever the circumstances behind its establishment, Mihama Academy is at present home to five female students, all with their own reasons for "enrollment." For better or worse, each girl has established a routine obliging of her current situation; life moves at an idle, yet accommodating pace within the walls of Mihama. 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? And in the first place, just who is Kazami Yuuji? While the true nature of the "job" he is wont to alight to at the most haphazard of moments remains shrouded in secrecy, one thing is for certain - his encroachment upon the quiet orchard known as Mihama Academy will prove itself momentous in one way or another. And of course, one cannot discount the possibility that perhaps Yuuji himself carries the weightiest past of any of the students...

Roughly a year after his arrival at Mihama, Yuuji makes the unexpected decision to pursue promotion within CIRS. The action resumes with Yuuji in a meeting with JB at "corporate HQ," discussing the documents he submitted for review as a part of the promotion process - said documents pertaining to none other than Yuuji's own past. Meanwhile, back at the dorm, the girls find themselves unwittingly following along after Sachi and Makina restore the shredded rough draft of said documents. The irony, of course, being that prominent figures in Yuuji's past may just be continuing to exert their influence upon the present... Also includes after stories for all heroines from Grisaia no Kajitsu as well as other side stories.

Following the Heath Oslo incident, the existence of the US-Japanese anti-terror organization CIRS has become a matter of public knowledge. CIRS has been rebuilt from the ground up, and its most covert functions spun off to a new agency: SORD (Social Ops, Research & Development). The goal of SORD is to train a new generation of operatives to defend the country against future threats. To that end, the organization has established a series of schools up and down the country. Mihama Academy, more-or-less left to rot after its abrupt closure, has been given new purpose as one such 'specialist training school'. This new incarnation of Mihama Academy is home to a diverse group of students, who every day work to polish their unusual skills - sometimes on the job. Mihama now entrusts the misfit girls who attend it with guns and live ammunition. Paying their own safety no heed, these students are again and again plunged into dangerous extrajudicial missions - all for the good of the realm. "We've been granted a place in the world. That alone isn't enough - there wouldn't be any meaning in living, if that was all we had... It's not enough just to get by on the backs of others. I live by my own strength, and I fight to survive. Because only the survivors among us belong with the living..." No matter how much life grinds them down, what future awaits these girls, who've themselves chosen the path of the gun?