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.

Faceless shadow nobles living in a vast mansion, attended by living dolls who spend much of their time cleaning up the soot endlessly emitted by their mysterious masters. Follow the story of Emilyko, a young and cheerful living doll, as she learns her duties serving as the attendant for Kate Shadow-sama. (Source: MU)

Mysterious immortal humans known as "Ajin" first appeared 17 years ago in Africa. Upon their discovery, they were labeled as a threat to mankind, as they might use their powers for evil and were incapable of being destroyed. Since then, whenever an Ajin is found within society, they are to be arrested and taken into custody immediately. Studying hard to become a doctor, Kei Nagai is a high schooler who knows very little about Ajin, only having seen them appear in the news every now and then. Students are taught that these creatures are not considered to be human, but Kei doesn't pay much attention in class. As a result, his perilously little grasp on this subject proves to be completely irrelevant when he survives an accident that was supposed to claim his life, signaling his rebirth as an Ajin and the start of his days of torment. However, as he finds himself alone on the run from the entire world, Kei soon realizes that more of his species may be a lot closer than he thinks. [Written by MAL Rewrite]

Medaka Kurokami is, in the truest sense of the word, perfect. Beautiful, intelligent, and athletic, Medaka's dream is to make others happy. So when she runs for Student Council President of the prestigious Hakoniwa Academy, winning the election with 98% of the votes is only to be expected. The very first thing the boisterous new president does is set up the "Medaka Box," a suggestion box allowing students to submit any kind of request for assistance. Together with the cynical Zenkichi Hitoyoshi, her childhood friend who has been strong-armed into helping, Medaka fulfills these requests at a ridiculous rate. For every job completed, she adds flowers to the student council room, with the aim of filling the entire school. However, the two are about to find out that helping others may be a lot harder than they think as they begin to uncover a devastating plan centering on the academy and even Medaka herself! [Written by MAL Rewrite]