Grisaia no Rakuen picks off just where the previous episode, Grisaia no Meikyuu, left off. Kazami Yuuji has been detained on suspicion of terrorism. A video appears to reveal clear evidence that Yuuji did these activities, and he is being detained in prison by Ichigaya. Ichigaya is well aware that Yuuji did not commit the offences for which he has been charged. He did, however, fail to murder Heath Oslo, the terrorist organization's commander and the owner of a highly lethal weapon. Ichigaya, in reality, has their own intentions for Yuuji... But Yuuji's situation may not be hopeless. The Mihama Academy girls, like the mysterious new figure that comes before them, are not about to allow Yuuji be exploited for political advantage.