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.

In a small quiet village in the Ardennes, a sixteen-year-old girl disappears into the forest after calling her teacher in the middle of the night. Captain Gaspard Deker, a former soldier and newly arrived single father is conducting the investigation with Virginie Musso, the local cop. Also helping is the teacher, Eve Mendel, a solitary young woman with a mysterious past: she was found as a child by the villiage doctor wandering silently in the same forest.

The murder of a young girl shocks a small Japanese village, and the victim's mother is distraught when the classmates her daughter was playing with all claim not to remember the identity of the killer. In her anger, she puts a curse on them.

Freed after 20 years in prison, the child killer Guy Beranger found refuge with the monks in Vielsart, a small village in Belgian's Ardennes. He is placed under the protection of a young Federal Police's inspector, Chloé Muller. A little while after his release, a little girl disappears.