The protagonist (the player) is a 17-year-old boy named Kotaro who lives in modern-day Japan. One day, he is caught in a supernatural phenomenon in Shibuya and loses consciousness. When he wakes up, he finds himself in a setting reminiscent of a Japanese historical drama. Eventually, Kotaro learns from a "god" that he has been transported back in time to the Edo period as a soul, and that he is now in Yoshiwara, the pleasure quarter in Edo, the capital of 19th-century Japan.

Without knowing why he has arrived in this era or how to return to the modern world, Kotaro begins to wander around Yoshiwara in search of clues to unravel the "mystery." Soon, he encounters the murder of an oiran (courtesan) and takes on the role of a "detective" to solve the case. However, he is drawn into a series of grotesque murders.