Two years after the world is freed from darkness, a young dragon escapes and crashes to earth. Shu and Bouquet have joined Legolas' Sarbin resistance against General Logi. Shu leads a supply raid on a Rosekstan airship, then rides with Bouquet to investigate the crater, and encounter a mysterious boy named Noi. All three find themselves prey to a Rosekstan fleet. But a red dragon appears and decimates the Rosekstan forces. While evading the red dragon, Noi uses his Tosen Kyuden ability on Shu. With Noi's help, the Blue Dragon returns. After a fierce battle, Shu and Blue Dragon cause the red dragon to retreat.

During their search for Jiro, Shu runs across news of a small war about to happen between a Rosekstan sub fleet led by Captain Varenko and a small band of resistance led by Captain Crester (one of the surviving members of Grand Kingdom). The party continues forward anyway hoping not to get found, leading to the combination of Saber Tiger and Hippopotamus with the 'stealth mode'. During but a few moments, Crester's band of resistance were eliminated. It was then suddenly Micheal appears before Crester and grant him the power to call his own Wyvern-like shadow allowing him to devastate General Logi's sub fleet. Having found out that the shadow that Crester wields is different from the normal Shadows and the Artificial Shadows used by Grand Kingdom, Shu's party steps in to defeat Crester. After defeating Saber Tiger and Hippopotamus, Crester faces off against Shu and Blue Dragon. After Crester is defeated, Shu, Bouquet, and Marumaro learn about the 'Dragon scales' Mikhail handed out which can grant miraculous powers to the user. They then overhear one of the Rosekstan soldiers tell Captain Varenko that they lost contact with General Logi.

Kluke uses Phoenix's ability to teleport the group to General Logi's hideout. When Shu shouts for a meeting with General Logi, he manages to allow it since he noticed Andropov with them. While Shu and Co. are talking with General Logi, Delphinium and Deathroy infiltrate General Logi's hideout looking for info that will help the White Guardians. As Shu and General Logi continue their conversation, one of Logi's men enters informing them that the White Guardians is attacking the Rosekstan forces. General Logi and Matilda leave as Andropov goes after them. As Delphinium and Deathroy find a room with giant exo-suits, General Logi talks with Andropov where the General still supports Andropov when he feels bad about what happened to Schneider. Shu and Blue Dragon leave to help the forces of Rosekstan fight the forces of the White Guardians. Blue Dragon destroys their Brunacks upon arrival. Outside of General Logi's hideout, Noi notices the White Guardians forces approaching in large numbers.