Bakumatsu: Crisis takes place during a pivotal era in Japanese history when young men were deeply concerned about the country's future. The story revolves around Takasugi Shinsaku, a soldier from Choshu who joins forces with Katsura Kogorou to retrieve a powerful time-manipulating artifact. Initially, Takasugi aims to destroy the artifact to prevent it from falling into the wrong hands, but the plan is compromised when it's stolen, prompting the duo to track down the thief in Kyoto. The city they find is drastically altered, with the government overthrown and the deity Susanoo holding power, forcing Takasugi and Katsura to reassess their mission and work towards resetting time to save their nation.