Saya Otonashi has been living the life of an anemic amnesiac, but otherwise ordinary schoolgirl. However, her happy life is shattered when she is attacked by a Chiropteran, learning that she is the only one who can defeat them. Armed with her special katana, Saya embarks on a journey with her family, allies, and her chevalier Haji, to rid the world of the Chiropteran threat and recover her identity. The course of the journey reveals the background history of the Chiropterans and Saya's past, which extends into the mid-19th century.