The story begins on October 4, 1986 at Rokkenjima, a private island where the wealthy Ushiromiya family have gathered to discuss the division of assets belonging to the ailing family head, Kinzo. Returning after a six-year absence, Kinzo's grandson, you becomes reacquainted with the legend of the "Golden Witch" Beatrice, who supposedly gave Kinzo ten tons of gold to restore his financially crippled family in the past. Beside her portrait is a riddle-like epitaph, which is believed to grant the rumored gold and the succession of the headship to the solver. A typhoon traps the eighteen people on the island, and occult-like murders occur in accordance with the epitaph, often in ways that seem impossible for a human.

At the end of the first game, the witch Beatrice seemingly kills and revives everyone. Refusing to acknowledge the existence of magic, you’re sent to the parallel dimension of Purgatorio, from which events on Rokkenjima can be seen. You face Beatrice in games of logic in subsequent episodes, with the murders repeating themselves in different ways each time, and is tasked to explain them all with human tricks. Over the course of the story, you come to understand magic as an adornment of reality with fantasy, used by several individuals as a coping mechanism for their harsh life situations, and how this is related to Beatrice.