The story of Rainbow Samurai takes place in mid-19th century Japan, a time of limited contact with the outside world and the beginning of Shogun Tokugawa's regime. Ryoma, a young boy living on the island of Shikoko, is a member of a lower-class samurai family. As he grows into his teenage years, Ryoma becomes disillusioned with violence and brutality, characteristics he often sees in the world around him. His older sister is the only one who truly understands Ryoma's sensitive nature and unique gift, and she works to support and protect him.