Continuing from the events of Grisaia no Meikyuu, Grisaia no Rakuen picks up with Kazami Yuuji's sudden arrest on terrorism charges. Despite a video supposedly incriminating him, Ichigaya, the arresting agency, is aware of his innocence in the alleged crimes. However, Yuuji did fall short in his mission to eliminate Heath Oslo, the dangerous leader of a terrorist group possessing a deadly weapon. While Ichigaya harbors undisclosed intentions for Yuuji, hope remains as the girls from Mihama Academy refuse to let him become a political pawn. A mysterious new presence further complicates the unfolding scenario, offering a glimmer of potential salvation for Yuuji.