Ryu Hyabusa returns once again. Set six months after Ninja Gaiden Black, Hyabusa must rescue a fellow female ninja named Momiji from the clutches of the evil Black Spider Ninja Clan and their leader, Obada. Along the way, Ryu must learn the secrets of the Dark Dragonstones and their relation to the Eye of the Dragon, which Obada hopes to posses in order to unleash an ancient evil named Ishtaros.
The gameplay consists of holding the DS like a book, using the stylus pen, tapping on the screen to move and using the pen to slash across enemies to attack and drawing symbols to use magic called Ninpo against them. The buttons on the DS are used for defensive stands.