Hanabishi Recca is a boy who emulates the ninja of the past. He is nearly killed in an accident, but a girl named Yanagi heals him with her powers. Later, the two are tracked down by a woman, who subsequently attacks them. Yet, just as the woman hurts Yanagi, Recca releases a powerful flame upon her, who is excited to see this. It turns out that Recca was born into the Hokage Ninja Clan of feudal Japan, and was sent to the future whilst still an infant in order to escape death. Now, Recca must use the legacies of his heritage to stop his half brother, Kurei, from kidnapping Yanagi.