Two years have passed since the war against Darkness. Shu and his friends have formed a Resistance group and continue their battle against the Rosenkroitz army led by General Logi.
A new threat arrives with a mysterious object suddenly falling from the sky. Shu and Bouquet run to the scene and meet a boy named Noi. Although they have never met, Noi seems to know Shu by his name and arrogantly tells him that Shu will be killed soon. Before they can question Noi what he means, a giant dragon suddenly appears and starts attacking them. In their desperate struggle, Noi uses his special ability and Blue Dragon is resummoned once again from Shu's shadow.
With new friends to travel with and new mysteries to solve, a new chapter of fantasy adventure BLUE DRAGON begins!