Once believed to be extinct, ninjas have reappeared in contemporary Japan following the Pacific War. With a headcount rumored to be two hundred thousand, these deadly assassins are now tasked with covert operations, infiltrating a significant portion of the nation's public and private institutions in the process.

Among these ninjas is Kurou Kumogakure, who often spends his days in a run-down apartment with no motivation to do much of anything. Some might consider him a useless vagrant who does nothing but steal beer from his neighbor. Nevertheless, the 17-year-old loser might actually be more dangerous than his demeanor suggests. Kurou's hidden potential is put to the test when he is given a new mission to infiltrate a local high school, but there is more to this assignment than he could ever predict.