Yukimura Chizuru is the daughter of a doctor who works in Edo; her father leaves Edo to work as a volunteer doctor and moves to Kyoto without his daughter. As time passes by, Chizuru starts worrying about losing contact with her father, so she decides to go to Kyoto in search of him.
On the way, Chizuru is attacked by few criminals and witnesses a fight between an oni and the Shinsengumi. Taking her into custody and saving her, the Shinsengumi debate on what to do with Chizuru when they discover that she is the daughter of the doctor they are also looking for. So they decide to become Chizuru's protectors and help her look for her father (the doctor).
Lots of events happen while she stays with the Shinsengumi, as they discover mysterious secrets and also fight against the Bakumatsu group.
En route to the capital, Serizawa Kamo, one of the Miburoushigumi leaders comes across Ibuki Ryuunosuke who had been attacked by bandits.
The Roushigumi are a group of people who share the same ideals, working towards the goal of becoming true samurai. As he observes the efforts of Kondou Isami and Hijikata Toshizou as they work to improve the prestige of the group, Ryuunosuke, who despises samurai, begins to question his way of life.
[Season 3 of Hakuoki, it is set before the first season.]