In the days of war, a baby fused together with a "shadow" called Blue Dragon, a legend among the "shadows". Because of that, he was locked in darkness from birth until recently, 15 years later, to prevent his shadow from activating. From the beginning, the only person he knew was his tutor who would come see him everyday. But "shadows" have begun to run rampant as they escape from "Noir" through living beings. Humnas call for the release of Blue Dragon in order to help mankind; thus their journey begins to seal the "shadows" along with the strongest: their queen.