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.

It is the day of the school festival, and Junichi Hashiba and Yukana Yame's class cafe is doing well. During a break from her shift, Yukana hears an urban legend about the festival’s after-party. According to the tale, couples who share the last dance together will be lovers for the rest of their lives. Unfortunately, others catch on to this rumor and decide to separate Junichi and Yukana before they can dance. Will the two be able to stick together, or will someone else whisk them apart?

Rumors about a potential plot to dismantle the Shinsengumi by setting fire to their headquarters have spread amok. As most of the talk stems from an inn in Shimabara, the Shinsengumi place trust in Chizuru Yukimura for help with the investigation. Disguised as a geisha, Chizuru infiltrates the inn to provide intel for the Shinsengumi but quickly finds that the operation is more intricate than they could ever imagine. At the same time, each member of the Shinsengumi has their own reservations and concerns about using their sole female colleague to gather intelligence. Knowing what dangers await her, they all resolve to protect her at any cost.

Special episode included in the second Blu-ray/DVD volume.