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.

Second year high school student Ichirou Satou has always been an average person—that is, until he runs into some not-so-average situations with his teacher, Kana The Demon Kojima. Kojima is Satou's Japanese language teacher with a reputation for being so ruthless that even school delinquents bow down to her. One fateful day, things escalate when Satou runs into Kojima in the restroom, leading them to share an intimate encounter that makes his imagination run wild for days after. Nande Koko ni Sensei ga? follows the daily life of Satou and his teacher as they continue to meet under similar conditions, growing ever closer with each encounter.

Rentarou Aijou has it all: looks, intelligence, athletic skill, and popularity with peers and mentors alike. Unfortunately, none of these qualities help Rentarou with his love life. On the day of his middle school graduation, he is once again turned down by a girl he confesses to, earning his one-hundredth rejection in a row. Down on his luck, he goes to a matchmaking shrine and wishes to finally get a girlfriend in high school. When the god of the shrine suddenly appears before him, Rentarou is told he will meet an astronomical total of one hundred soulmates in high school. Though Rentarou initially does not take this foretelling seriously, his doubts disappear when, on the first day of school, he meets two of these soulmates—Hakari Hanazono and Karane Inda—who both confess to him. With fated encounters and love confessions galore, Rentarou's life is about to get a lot more exciting.

Having attended Mihama Academy for about a year, Yuuji Kazami has seemingly found his place within the school, but he suddenly decides to pursue a promotion in CIRS. After consulting JB about his intentions, they both thoroughly examine Yuuji's documents and dissect the events of his upbringing to determine if the job is fit for him. Meanwhile, unbeknownst to the two, the girls of Mihama uncover some torn documents in Yuuji's room. After restoring the papers, they discover the story that has formed—or perhaps broken—Yuuji into the man he is today. However, what was thought to be history has haunted him to the present, and the chains of the past begin to drag him back into the darkness...