The Sonozaki family of Hinamizawa has kept twin sisters Mion and Shion apart for as long as they can remember. Mion will become the next heir of the Sonozaki family, and Shion will attend St. Lucia Academy, away from her dear sister and their relatives. But Shion escapes the school and returns to Hinamizawa, unaware of the cruel tragedy awaiting her.

When she reunites with her sister and gets a part-time job—while pretending to be Mion—she meets Satoshi Houjou, a boy her age with whom she falls madly in love. But when she learns about Satoshi's horrible family situation, she begins to resent everyone in his household—even his younger sister, Satoko. When tensions escalate and Satoshi abruptly goes missing, Shion begins to suspect that her own family may have had something to do with his disappearance.

A year later, Shion meets Keiichi Maebara, Mion's crush. Her sister's infatuation with Keiichi stirs up her old feelings for Satoshi, and awakens a vicious desire to find out the truth behind his disappearance once and for all. However, Shion's quest for the truth will send her spiraling down a dark path of madness and despair.