Ten years prior to the events of the game, five young girls were kidnapped by You Haibara, a criminal, from a mysterious sanatorium on Rougetsu Island. They were eventually rescued by Choushiro Kirishima, a detective pursuing the criminal. Several years after the incident, two of the girls (Marie Shinomiya and Tomoe Nanamura) died mysteriously. The three remaining girls, Misaki Asou, Ruka Minazuki and Madoka Tsukimori, now seventeen years old, return to the island to recover their lost memories and find out more of what happened that day. Choushiro continues to pursue Haibara, as well as aiding Ruka along the way.