The game takes place in a re-imagined late 16th century Sengoku period Japan. At the end of the Sengoku era, warlord Isshin Ashina stages a bloody coup and seizes the land of Ashina. During this time, a nameless orphan is adopted by the wandering shinobi Owl, who names the orphan "Wolf".

Twenty years later, the Ashina clan are on the brink of collapse due to a combination of the now elderly Isshin having fallen ill and the clan's enemies steadily closing in from all sides. Desperate to find a way to prevent the fall of his clan, Isshin's grandson Genichiro captures the Divine Heir Kuro, in hopes of using his "Dragon Heritage" to create an immortal army.