Kivotos is a federal megalopolis comprising thousands of schools and is led by the General Student Council (GSC), which acts as its governing body. Ironically, despite being an academy city, Kivotos is rife with gun violence, and all students wield firearms as part of their everyday lives. As if the crisis in Kivotos was not enough, the GSC president is nowhere to be found. Fortunately, before her sudden disappearance, the GSC president enlisted the help of Sensei—a teacher who is most likely the only one in Kivotos—to support students in their time of need. Sensei's first course of action is to assist Abydos High School, a once prestigious academy now with merely five students in attendance. These remaining students are doing everything they can to pay their academy's crippling debt of almost one billion yen.

The story takes place in Japan. The year is 2030 and Earth has been completely overrun by a viral disease named "Gibia" that turns infected people into various different monsters, based on their age, sex, and race. A samurai and a ninja from the early Edo period travel together through time and arrive in a ruined Japan to aid a professor working on a cure for the virus. Together, they fight countless Gibia monsters, outlaws, and other fierce foes on their journey to save mankind.