Hakuouki is set in Japan in 1864, where Chizuru Yukimura leaves home disguised as a man and travels to Kyoto in search of her missing father, Koudou. A doctor whose work often takes him far from home, Koudou has gone months without sending word, leaving Chizuru with no choice but to look for him herself. In Kyoto, her attempt to stay hidden draws the attention of ronin, and she witnesses a horrifying scene as the men are brutally murdered by crazed white-haired attackers. Before Chizuru can escape, members of the Shinsengumi arrive and cut down the creatures, then tie her up and bring her back to their headquarters, unsure whether to let her live or silence her permanently.
Once she reveals her father's name, the Shinsengumi realize they have been searching for Koudou as well and decide to protect her. Under the command of Toshizou Hijikata, with fighters such as Souji Okita and Hajime Saitou at the forefront, the group becomes both Chizuru's refuge and her link to a widening mystery. Koudou is more connected to the Shinsengumi than they initially admit, and Chizuru becomes caught between the Shinsengumi and their enemies as political tension spreads through Kyoto. The series blends Bakumatsu-era conflict, romance, and supernatural intrigue as Chizuru is drawn deeper into the Shinsengumi's battles and the secrets surrounding the white-haired men.