The series is initially set in September in Okinawa City (Koza) on Okinawa Island near the US Kadena Air Base. Under the care of her adoptive family, the protagonist Saya Otonashi had 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, a hematophagous bat-like creature that lives by feeding on human blood. Saya learns that she is the only one who can defeat them, as her blood causes their bodies to crystallize and shatter. 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. Over the course of the series, Saya travels across the world from Japan to Vietnam, Russia, France, and finally the U.S.