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]

Following the events of "Scorched Halloween," the world is introduced to a terrifyingly powerful Strategic class magician. In an effort to uncover the identity of this person, the United States of the North American Continent (USNA) dispatches the most powerful asset in its arsenal to Japan on a covert mission—the elite magician unit "Stars" and its commander, Angie Sirius. At First High School, Tatsuya Shiba and his friends are having a farewell party for Shizuku Kitayama, who is leaving to study abroad in the USNA as part of an exchange program. In her place, the group welcomes the beautiful Angelina "Lina" Kudou Shields. Around the same time, Tatsuya is informed about the USNA's plan to uncover his true identity. Elsewhere in Tokyo, numerous reports arise of seemingly random bodies found drained of blood. Dubbed as the works of a vampire, it does not take long for Tatsuya to connect the dots and realize that it is almost impossible for the timing of these events to be mere coincidences. [Written by MAL Rewrite]