A significant amount of time after the events of Ninja Gaiden 3, as the Dark Dragon was seemingly slain, its remains cause the Rain of Darkrot over Tokyo, indicating the divine dragon still lives. Yakumo, a young ninja from the Raven clan - a rival of the Hayabusa clan - dives into the ruined capital to assassinate the Dark Dragon Priestess Seori in order to fulfill his clan's prophecy. However, not is all as it seems; and in exchange for sparing her life, Seori offers to assist in undoing the seal so that Yakumo may slay the Dark Dragon once and for all.
Standing in Yakumo's path are the Divine Dragon Order, an organization responsible for policing the desolate city. This group guards the Seal of the Dark Dragon, and controls a horde of Fiends lurking through the world.
