The beginning of Grisaia no Rakuen picks up where Grisaia no Meikyuu left off. Kazami Yuuji is detained by Ichigaya under suspicion of terrorism due to a video that showcases what appears to be indisputable proof of his guilt. Despite being aware of Yuuji's innocence, Ichigaya recognizes that he was unable to complete his mission to assassinate Heath Oslo, the leader of a terrorist group with a dangerous weapon. As a result, Ichigaya has its own agenda for Yuuji. But Yuuji still has a chance. The female student body at Mihama Academy is determined to prevent him from being used for political gain, and a mysterious figure steps up to aid their cause.