The story of the Blue Dragon saga centers on a young boy named Shu and several of his friends who possess the ability to control phantom shadows that mirror the actions of their masters. In Blue Dragon Plus, one year has passed since Shu and his companions defeated the tyrannical remnant of the Ancients, Nene. In the midst of the battle, the world split in two and now consists of a myriad of "cubes" that exploded from its depths. King Jibral notices a mysterious cube in the distance suddenly start to move violently, and from it he sees the Shadow of a Balaur, a three-headed dragon, emerge. The enormous and sinister Shadow is just the beginning of the new turmoil and devastation to come!