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.

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]

Short specials included in the Blu-ray and DVD releases.

A heated battle is once again revving up at Basara Academy between baseball star Masamune Date and soccer ace Yukimura Sanada. What's more, ever since student council chairman Hideyoshi Toyotomi received a suspension, leaving the seat up for grabs, a host of class "warlords" have become embroiled in a quest for supreme power. Amid Ieyasu Tokugawa's appeals to bonds of kinship and Mitsunari Ishida's fervor to defeat him, who will wrest ultimate control of the domain in "troubled" times? (Source: TBS Global Business)