In the beginning, all was dark and formless. From this formlessness arose the Dragon Saints, keepers of the elements who in unity created the world. As ninja clans were formed under each saint, conflict arose but was ended by the legendary ninja Gaiden after he defeated the evil Samurai warrion Shekan. Many centuries later, two brothers, Ryu and Michael discover a forbidden secret passage within the Temple of their village resulting in the destruction of their village. Thus begins their quest to assemble the human and dragon saints of the elements and foil the ambitions of the Dark ryu who intend to unseal an ancient evil warrior. However, as it turns out, the journey is more than a quest of vengeance and will lead to the revelation of secrets concerning the very origin of their world and an even more threatening evil.