The narrative is set in Nagasaki prefecture, in Minami Shimabara city, the reputed birthplace of the Shimabara Rebellion, which shook Japan in the early Edo era. It is also where Shirou, a third-year junior high school student, spends his days with his classmates. Shirou's elder childhood friend Akane arrives to Minami Shimabara from Tokyo one summer day. Shirou and Akane go for a walk in Minami Shimabara with another old buddy, Tokiya. While these buddies are grappling with memories and more complicated emotions, a weird monster known as Goron emerges in front of them. This meeting with a tiny small creature sets off a chain of events in this metropolis...