Great Japan is the envy of all other countries, with its beautiful terrain and rich people. However, a significant threat looms over the country. Master Samurai, or mysterious guardians, are Great Japan's sole protection. Muneakira Yagyuu, a young samurai, arrives at Buou Academic School at the request of the student council. The Tokugawa Shogunate runs the school, where children of samurai get the aristocratic education necessary to manage the kingdom. Yoshihiko Tokugawa, the student council president, and his sister Sen, Muneakira's childhood friend, lead the school. When Muneakira arrives to the academy, he finds himself in the middle of a horrible struggle. During the pandemonium, the sky is filled with a strange white light, and a mysterious girl named Juubei Yagyuu appears.