Grisaia no Rakuen begins right at the end of the previous installment, Grisaia no Meikyuu. Kazami Yuuji is arrested under suspicion for terrorism. A video showing apparently concrete proof that Yuuji committed these acts, and he is held in custody by Ichigaya. Ichigaya knows full well that Yuuji didn't commit the crimes he has been accused of. But he did fail to assassinate Heath Oslo, who is the leader of the terrorist organization with an extremely devastating weapon in their possession. In fact, Ichigaya have their own plans for Yuuji... But all may not be lost for Yuuji. The girls of the Mihama Academy are not about to let Yuuji be used for political gain, and neither may the mysterious new figure which appears before them.

A bus full of eccentric individuals is headed towards the urban legend known as Nanaki Village, a place where one can supposedly start over and live a perfect life. While many have different ideas of why the village cannot be found on any map, or why even the police cannot pinpoint its location, they each look forward to their new lives and just what awaits them once they reach their destination. After a few mishaps, they successfully arrive at Nanaki Village only to find it completely abandoned. Judging from the state of disrepair, it has been vacant for at least a year. However, secrets are soon revealed as some of the group begin to go missing while exploring the village and amidst the confusion, they find bloody claw marks in a forest. As mistrust and in-fighting break out, will they ever be able to figure out the truth behind this lost village? [Written by MAL Rewrite]

In a research facility hidden away on a remote island, genius programmer Shiki Magata has lived as a recluse for years. She rarely sees guests, but associate professor Souhei Saikawa and university student Moe Nishinosono still seek her out. However, their meeting is cut short when they are caught up in a locked-room murder mystery. Everything is not as it seems, and many secrets are hidden. Within an isolated facility, a seemingly impossible and gruesome crime takes place, and Saikawa and Moe must unravel the truth behind the murder and Magata's shrouded past. [Written by MAL Rewrite]

Surrounded by a forest and a gated entrance, the Grace Field House is inhabited by orphans happily living together as one big family, looked after by their "Mama," Isabella. Although they are required to take tests daily, the children are free to spend their time as they see fit, usually playing outside, as long as they do not venture too far from the orphanage—a rule they are expected to follow no matter what. However, all good times must come to an end, as every few months, a child is adopted and sent to live with their new family, never to be heard from again. However, the three oldest siblings have their suspicions about what is actually happening at the orphanage, and they are about to discover the cruel fate that awaits the children living at Grace Field, including the twisted nature of their beloved Mama. [Written by MAL Rewrite]