Season 1 :
In 1864 Japan, a young woman named Chizuru Yukimura is searching for her missing father, Koudou, a doctor by trade whose work often takes him far from home. But with no word from him in months, Chizuru disguises herself as a man and heads to Kyoto in search of him. Attracting the attention of ronin, she tries to hide and ends up witnessing a horrifying sight: the ronin being brutally murdered by crazed white-haired men. In a startling turn of events, members of the Shinsengumi arrive to dispatch the creatures. But Chizuru's safety doesn't last long, as this group of men tie her up and take her back to their headquarters, unsure of whether to let her live or silence her permanently.
However, once she reveals the name of her father, the Shinsengumi decide to keep her safe, as they too have been searching for him. But Koudou is more connected to the Shinsengumi than they let on, and soon Chizuru finds herself embroiled in a conflict between the Shinsengumi and their enemies, as well as political tension in Kyoto.
Season 2 :
After the conclusion of Hakuouki, Chizuru Yukimura and the Shinsengumi are forced to flee Kyoto and set sail for Edo. In their commander Isami Kondou's absence, vice-commander Toshizou Hijikata steps in as acting commander. However, Hijikata is not only struggling with the extra leadership duties—which worries everyone around him—but also a newfound uncontrollable bloodlust. To make matters worse, the urge does not affect him alone, and it is even beginning to drive some of his subordinates mad.
Finally, Kondou returns with orders from the emperor to defend the castle, and a new name for their squad: the Kouyou Chinbutai. But in war, the balance of power can shift suddenly and allegiances can waver. In Hakuouki Hekketsuroku, Chizuru follows the Shinsengumi into the heart of war and continues the search for her missing father, all while the bond between her and Hijikata grows ever stronger.
Season 3 :
The year is 1863 and as Japan's long festering wounds of political discord erupt into violent waves of street clashes and murder, the Tokugawa Shogunate sends a new force of masterless samurai called the Roshigumi to the aid of the Aizu forces in Kyoto. However the new "police" are anything but a cohesive force and assassination has already split them into two opposing factions. The stronger is led by the brutal Serizawa Kamo and the lesser by the more honorable but less assertive Isami Kondo. It is into this pack of wolves that Ryunosuke Ibuki is dragged by the rabid Serizawa. Forced to be a virtual slave by blood debt, he hates the samurai and everything they stand for. But as he sees how the other half of the samurai live, he begins to believe that there may still be a chance, for both himself and Japan, if only Kondo will step up and take down the mad dog Serizawa!