Several years after The Fruit of Grisaia... What was once Mihama Academy, a sanctuary for young girls, has now been transformed into a SORD (Special Organization for Research & Development) training school dedicated to fostering talent for national defense. Rena and Maki specialize in firearms, Tohka and Gumi excel at sniping, Chris handles explosives and data processing, and Murasaki is a skilled ninja for intelligence operations. Together, they take on cases too complex for the police or Self-Defense Forces, repeatedly facing dangerous missions. This is the story of these young girls, painted in blood and gunpowder. (Source: Crunchyroll)

Life is not going well for 28-year-old Kyouya Hashiba. Having left his office job to pursue a career in the video game industry, his internship at a popular game studio abruptly ends, leaving him unemployed and forcing him to move back in with his parents. Additionally, his jealousy toward the success of the Platinum Generation—a group of similarly-aged creators—has caused him to regret his decision to attend a traditional university instead of an arts college. Even though he believes there are no second chances in life, Kyouya is suddenly given one when he wakes up one day and finds himself 10 years in the past. Instead of choosing business school like he originally had, Kyouya decides to pursue his passions and attends the Oonaka University of Art. There, he meets classmate Eiko Kawasegawa, the woman who had hired him as an intern in the present, alongside his new housemates and future Platinum Generation members: underachieving artist Aki Shino, aspiring singer and actress Nanako Kogure, and naturally-gifted writer Tsurayuki Rokuonji. With each project they complete together, Kyouya and his friends venture closer to discovering their true potential as creators and remaking their lives into the ideal versions they desire.

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...

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.