Silent, apathetic, yet mischievous, 14-year-old Rokujou Miharu is the bearer of the hijutsu 'Shinrabanshou,' a powerful technique many ninja clans desire so they can become the ruler of Nabari. His classmate Kouichi Aizawa and English teacher Thobari Durandal Kumohira are both secretly Banten clan ninjas who have pledged themselves to protect Miharu from his many attackers. Keeping apathetic, Miharu attempts to reject their invitation to join their ninja 'club.' However, after numerous attacks, he finds no choice but to join their group as a means for his survival. Slowly, Miharu gets ever closer to becoming the ruler of Nabari.