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.