Following the conclusion of the Blue Dragon saga, Shu and Bouquet align with a rebel faction to combat General Rogi's invading forces. Their path intersects with a enigmatic youth named Noi, capable of resurrecting Shu's shadowy alter ego, Blue Dragon, and shielding her from the clutches of a scarlet dragon. Together, Shu and his comrades embark on a new expedition to unravel the enigma surrounding the dragons, face their trials, and prevent a series of ominous events that jeopardize humanity's future.