The game follows the ninja Ryu Hayabusa and shares its story with Ninja Gaiden II. Alongside Ryu's campaign, this version adds chapters starring three other playable characters. Ayane is a kunoichi from the friendly Mugen Tenshin ninja clan who aids Ryu. Momiji is a member of the Hayabusa clan who fights with a naginata. Rachel is a Fiend hunter from the Holy Vigoor Empire who carries the curse known as the Fiend's Blood.