Glass Rose primarily takes place in a remote Japanese mansion in 1929. The player assumes the role of an amateur reporter named Takashi Kagetani. While exploring an abandoned mansion with his friend Emi in the year 2003, he is knocked unconscious by a supernatural force and awakens seventy years in the past, where the mansion has been restored to its former glory. In order to return to his own time, Takashi is forced to explore the mansion and interact with its denizens, the Yoshinodou family.
Takashi also finds that the time warp has left him with the ability to briefly glimpse into a person's mind while conversing with them. By employing this ability, he can investigate into a series of murders in the Yoshinodou household.