The story of a young boy Kamui growing up to become a ninja. His life of training ends when he realizes that he doesn't want to be a ninja and decides to become a nukenin (outlaw ninja), someone who is not affiliated with an organization and is hunted for leaving the clan...

A side story of the larger Kamui Den series, Kamui Gaiden deals with the adventures of the fugitive ninja Kamui as he befriends a fisherman's family and battles antagonizing ninjas.