Yuuji Kazami is a transfer student who has just been admitted into Mihama Academy. He wants to live an ordinary high school life, but this dream of his may not come true any time soon as Mihama Academy is quite the opposite. Consisting of only the principal and five other students, all of whom are girls, Yuuji becomes acquainted with each of them, discovering more about their personalities as socialization is inevitable. Slowly, he begins to learn about the truth behind the small group of students occupying the academy—they each have their own share of traumatic experiences which are tucked away from the world. Mihama Academy acts as a home for these girls, they are the "fruit" which fell from their trees and have begun to decay. It is up to Yuuji to become the catalyst to save them from themselves, but how can he save another when he cannot even save himself? [Written by MAL Rewrite]

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]