Grisaia centers on Yuuji Kazami, a transfer student who arrives at Mihama Academy expecting the ordinary high school life he has never really had. Instead, he finds a school that barely resembles one at all: the campus is inhabited by the principal and five other students, all of them girls, and every one of them is carrying a trauma carefully kept away from the outside world. In Grisaia, Mihama becomes a refuge for people who have fallen out of the lives that once supported them, a quiet place where survival, trust, and the possibility of starting over are all fragile at best.
As Yuuji settles in, the strange calm of the academy slowly gives way to deeper questions about why these girls are there, what they are trying to escape, and how much of themselves they can afford to reveal. The "fruit" of Mihama are girls who have fallen far from the branches that once held them, and the series traces the painful, careful bonds that grow between them and the one person who may be able to help. Yet Yuuji is not simply a rescuer. He is burdened by wounds of his own, and Grisaia asks whether he can protect others without first confronting the parts of himself he has tried to leave behind.