Under the care of her adoptive family, Saya Otonashi has been living the life of an anemic and amnesiac, but otherwise ordinary schoolgirl. Saya’s happy life is shattered when she is attacked by a chiropteran, and learns that she is the only one who can defeat them. ("Chiroptera" is the name of the order of biological classification that contains bats, probably the reason for the vampiric creatures being called "Chiropterans".)

Armed with her sword, Saya embarks on a journey with her family, allies, and Chevalier, Haji, to rid the world of Chiropterans and rediscover her identity. The course of the journey reveals the background history of the chiropeterans and Saya's very deep past, which extends into the mid-19th century.