When Kōichi Sasakibara transfers to his new school, he can sense something frightening in the atmosphere of his new class, a secret none of them will talk about. At the center is the beautiful girl Mei Misaki. Kōichi is immediately drawn to her mysterious aura, but then he begins to realize that no one else in the class is aware of her presence.
Asahioka Branch School, a combined elementary and middle school in an isolated village, has only five students total, four girls and one boy. The girls are best friends, and pass the season with traditional activities like harvesting mountain herbs and fishing.
Sotobamura is a small village with around 1300 residents; so small the village isn't even connected to a single highway. An isolated village in which old customs, such as the burial of the dead, are still practiced. One day, the bodies of three people are found dead. Although Ozaki Toshio, the village's lone doctor, feels uncertain, he treats the deaths as a normal occurrence. However, in the days following, the villagers start to die one after the other.
After moving into the quiet town of Hinamizawa, Maebara Keiichi spends his days blissfully in school often playing games with his local friends. However, appearances can be deceiving. One fateful day, Keiichi stumbles upon news of a murder that had occurred in Hinamizawa. From this point on, horrific events unfold in front of Keiichi, as he soon learns his close friends may not be all that they seem. Based on the amateur mystery game by 07th Expansion, the story is told in a series of different scenarios.