The series follows the adventures of American Veteran, John Peter McAllister, who stayed in Japan after World War II and has learned the art of ninjutsu. Years later he leaves Japan to find his long lost daughter, on his journey he meets Max Keller who insists on learning John's ninja skills. Each episode they travel to a new area and help those in need and also encounter many threats including John's rival Okasa.

The series appeared as two TV movies Master Ninja and Masters Ninja II on the show Mystery Science Theater 3000, episodes 322 and 324.