Miyoko Tanashi lived a charmed life with her parents, but after losing both of them in a devastating train accident, the life she knew was suddenly ripped away. Sent to a secluded orphanage in the mountains, she is subjected to inhumane abuse at the hands of her caretakers; escape is not an option since runaways are met with a fate far worse than death. But eventually, Miyoko manages to flee and receive aid from her father's mentor—a researcher named Dr. Hifumi Takano.

Adopted by Hifumi and finally free from her hell, Miyoko takes on a different identity to go along with her new life. When Hifumi's research on a mysterious disease in a mountain village is ridiculed, Miyoko makes it her life's work to prove that the disease truly exists. However, her mission soon turns into a deadly obsession once she arrives in the village, as she is more than willing to prove the doctor's findings by any means necessary...

In the conclusion to the Higurashi story, warring fates and indomitable wills clash in this final confrontation in June of 1983.