"Bakumatsu" is set during the Bakumatsu period in Japan, a time of political upheaval and transition from the Tokugawa shogunate to the Meiji Restoration. The story intertwines historical events with fictional elements, blending action, drama, and supernatural themes. The narrative centers on two protagonists: Hijikata Toshizō, the vice-commander of the Shinsengumi, a pro-shogunate police force, and Sakamoto Ryōma, a revolutionary figure advocating for modernization and the overthrow of the shogunate. Despite their opposing ideologies, both characters are drawn into a larger conflict involving a mysterious artifact known as the "Grimoire," which possesses the power to alter history.

The Grimoire becomes the focal point of the story as various factions, including the Shinsengumi, the Ishin Shishi (pro-imperial loyalists), and other shadowy groups, vie for control of its power. The artifact's abilities attract the attention of supernatural entities and time travelers, further complicating the political and social turmoil of the era. As the story progresses, Hijikata and Sakamoto find themselves reluctantly working together to prevent the Grimoire from falling into the wrong hands, recognizing the catastrophic consequences it could unleash on Japan's future.

The series explores themes of loyalty, sacrifice, and the clash between tradition and progress. Supporting characters, such as Okita Sōji, a skilled swordsman and member of the Shinsengumi, and Oryō, a spirited woman with ties to Sakamoto, add depth to the narrative. The interplay between historical accuracy and creative liberties creates a dynamic backdrop for the characters' personal struggles and the broader societal changes of the Bakumatsu period. The story balances intense action sequences with moments of introspection, highlighting the moral ambiguities faced by individuals caught in the tide of history.