Samurai Princess takes place sometime, somewhere in an alternate universe version of a feudal Japan where people live together with highly developed mechanical dolls. These excessively developed mechanical dolls start causing harm to the human society leading to a ghastly bloodshed. It is under these circumstances that Kyoraku, a mad scientist, creates a mechanical female ninja. Equipped with eleven types of built-in weapons, the ninja doll is also infused with the souls of eleven of her fallen sisters. She uses their combined power to take down anyone who stands in her way. Virtually indestructible, the ninja is on a quest to save humanity.