When many deaths occur in the quiet village of Sotoba, Doctor Toshio Ozaki initially suspects an epidemic but soon becomes convinced that something else is causing them.

Shizuku, a hardworking student who isn't interested in socializing, finds an unlikely friend, Haru, an emotionally volatile boy at her school.

An unnamed girl acts as a mediator between humans and "fairies" after they have become the most prosperous species following the decline of the human population.