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.

In the nineteenth century, we find Lydia Carlton living in Scotland, making a living as a fairy doctor. She is one of those rare humans who can see and communicate with fairies. But no one believes her. However, Edgar is in need of someone with a vast knowledge of fairy lore, and Lydia is just that person. After rescuing her, he becomes her employer, but there are many secrets and emotions that seem to follow Edgar, who claims to be the Blue Knight's Earl.

Chibi-Earl and Chibi-Fairy. Every special focuses on another character, who will in their turn recite a poem by Shakespeare, that they feel describes their lives the best.

Beaten and left to perish, Ryuunosuke Ibuki is robbed of everything to his name. Seeing him in such a pitiful state, a man named Kamo Serizawa gives him a second chance and offers him to become his personal assistant. Ibuki seems to be spared by grief, but this new lifestyle only makes him nothing more than a dog to one of the most influential men in all of Kyoto. Meanwhile, with the rise of ronin attacks on the general population, the shogunate sends the Roshigumi to Kyoto to strike for peace. Led by the honorable yet soft-spoken Isami Kondou, the Roshigumi is composed of strong and skilled samurai but lacks any meaningful political connections to gain footing in the city plagued by crime. Having no other choice, Kondou allies with the arrogant Serizawa and his connections in exchange for their combative strength. Despite hating everything the samurai stand for, Ibuki finds himself tangled in the business of the Roshigumi. However, as he interacts with the members under Kondou's leadership, Ibuki slowly realizes that not all samurai are as cruel and dishonorable as he once thought. Hakuouki Reimeiroku explores the early days leading up to the formation of the Shinsengumi while the political tension in Kyoto gives rise to instability and uncertainty.