Disguised as a boy, young Chizuru Yukimura leaves her quiet home and heads to Kyoto in search of her missing father—a medical doctor by the name of Koudou. She soon learns that the volatile capital city is a dangerous place to be in as she is ambushed by a pair of ronin while in the streets. Much to her horror, the ronin are slain right in front of her eyes by white-haired, red-eyed samurai, only to be quickly disposed of by three men from the Shinsengumi—a special police force who serve the shogun.

After the incident, Chizuru finds herself being taken into custody by the Shinsengumi for further questioning. Upon learning that her missing father is also the same man they are searching for, the chief allows her to stay in their care while they look for his whereabouts. While working as an assistant for second-in-command Toshizou Hijikata, Chizuru slowly discovers just how connected the troubling political environment of Kyoto and the demonic-looking white-haired samurai are to her.