The setting of Bakumatsu Renka Karyuu Kenshiden is during the initial year of Tokugawa, when a power struggle between the Shogunate and the emperor's allies ensues. The protagonist, Shizuki Rin, has amnesia and is raised in a dojo that operates covertly as an information hub. The dojo harbors members of the fierce Shinsengumi, attractive individuals, and aspiring children seeking to enhance their fighting capabilities.