Following the Blue Dragon series, Shu and Bouquet align with a rebel force to combat General Rogi's invading army. They come across a peculiar young girl named Noi who possesses the ability to resurrect Shu's shadow-like alter-ego, the Blue Dragon, and rescue her from a red dragon's pursuit. Now, Shu and his comrades must embark on yet another expedition to decipher the dragons' intention, endure their trials, and thwart the sequence of events that imperils humanity's destiny.