The series takes place in an alternate version of Japan called Great Japan, in an alternate timeline where the Tokugawa shogunate remained active and has remained isolated from the rest of the world. The story takes place at Buou Academic School, an academy located at the base of Mount Fuji where children of military families train to become samurai warriors. The academy is in the middle of a power struggle between Yukimura Sanada and Matabei Goto of the Toyotomi faction and the powerful student council that rules the school, and Muneakira Yagyu, the owner of the Yagyu Dojo, and the mysterious Jubei Yagyu are dragged in the middle of the conflict.