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.

Kouhei Araki, a veteran editor of the dictionary editorial division at Genbu Publishing, plans to retire in order to better care for his ailing wife. However, before retiring, he must find a replacement to complete his latest project: a new dictionary called "The Great Passage." But no matter where he looks, he cannot find anyone suitable, as making a dictionary requires a wealth of patience, time, and dedication. Mitsuya Majime works in Genbu Publishing's sales division, yet he has poor social skills and an inability to read the mood in most situations. In spite of this, he excels at having an enthusiasm for words thanks to his love of reading and careful personality. It is these skills that draw Araki to him and prompt him to offer Majime a position in the dictionary editorial department. As Majime accepts his new position, he finds himself unsure of his abilities and questioning whether he will fit in with his new co-workers. Yet amid the vast sea of words, The Great Passage will bring them together. [Written by MAL Rewrite]

Like many hardworking members of the workforce, Kuroto Nakano is perpetually stressed out by his job. Still, since he lives alone, he must carry on to sustain himself. Little do humans like Kuroto know, this stress takes the form of darkness residing within a person's body and will bring one's life to ruin. Fox deities can see this darkness and have the duty to save people before it is too late. To help rid Kuroto of his stress, Senko-san, an eight hundred-year-old foxgirl, volunteers to take care of him, and will do everything she can to ease the tension in his weary soul. [Written by MAL Rewrite]