The village of Ootsuka—home to Shino Inuzuka, Sousuke Inukawa, and Hamaji—was lit on fire under the preconception that a virus had seen all of its life eradicated. Now surrounded by flames and on the verge of death, the three were approached by a strange man holding a sword. He tells them that they must reach a decision if they want to live. That night changed everything for these children. Five years later, the family of three now lives under the watchful eye of the small Imperial Church in a nearby village. All is fine and dandy until the Church attempts to reclaim the demonic sword of Murasame. To accomplish this, they kidnap Hamaji to lure Shino, now a bearer of Murasame's soul, and Sousuke, who possesses the ability to transform into a dog. The brothers must put their differences aside to rescue their beloved sister from the Church in the Imperial Capital, signalling the beginning of a very difficult journey.

In a world inhabited by people only a few inches tall, young women Hakumei and Mikochi live together in a house built into a tree. Hakumei is an energetic and tomboyish carpenter, while Mikochi is a feminine and calm tailor. Despite their differences, they get along well and spend their days having fun living their lives in the woods. The two of them spend their time working, going on sightseeing adventures, and taking shopping trips into Tsumiki Marketplace by the ocean. They make many friends along the way, be they sentient woodland creatures like Iwashi the Weasel or fellow miniature people such as the songstress Konju and the inventor Sen. Hakumei to Mikochi is a relaxing look into the day-to-day lives of its titular characters as they explore and interact with their tiny world which seems to be straight out of a fairy tale.

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.

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.