Disguised as a man, Chizuru Yukimura has come to Kyoto searching for her missing father, a doctor who developed a magical elixir that increases the drinker's speed, strength and healing abilities. Instead of her father, however, she stumbles across a battle between the Shinsengumi and the Furies, evil vampire-like creatures of their own making. As things turn out, the Shinsengumi are also searching for her father. And when they discover who she is, they decide to take her into their custody for safe-keeping.
But her sex is not the only secret Chizuru has, and as more and more Furies begin appearing in Kyoto and the situation becomes ever deadlier, the Shinsengumi may find that the Furies are the least of their problems in Hakuoki!