The backdrop of Kidou Shinsengumi Moeyo Ken is the Meiji era, and the plot revolves around Kondou Yuuko, Hijikata Toshie, and Okita Kaoru - daughters of ex-Shinsengumi members. Following their fathers' footsteps, they have been enlisted to safeguard Japan against its current predicaments, including inexplicable supernatural events and other looming threats. Their mission is set in the Kyoto region, which they must shield from harm while dealing with paranormal occurrences.