Shu and his comrades wander into a town that has been decimated. A pint-sized Shadow wielder named Marumaro attacks them, convinced that they are enemies. Will Marumaro be convinced of Shu's innocence in time to save the villagers from the real invading army, and take on a pair of Shadow-wielding brothers at the same time?

Zola's group arrives at the Republic of Metia, the nation next to the Grankingdom. From there they hope to cross through a canyon into the Grankingdom, but General Logi is ready and waiting with an ambush. With the formidable Shadow wielders Gilliam, Cynthia and Lemaire against them, Shu and his friends find themselves in dangerous combat.

Shu's informant Homeron is gathering information about the Extra Seven. Shu and Co. arrive at Flame Phoenix ruins. When Kluke disappears, she ends up in the area where she first encountered her Phoenix shadow and asks it how she can call upon its power again. Phoenix tells Kluke that the answers lie in herself. Kluke then receives a necklace and rejoins Shu and Co. When they find Jibral's scattered army being attacked, Shu and Co. join the battle. Upon defeating the robotic soldiers and their shadows, Shu and Co. are soon attacked by a giant robot. Kluke brings out her Phoenix Shadow to use its barrier to protect everyone enough for Shu to use Blue Dragon to destroy the giant robot. Meanwhile, Homeron receives news the mysterious woman who stole the Extra 7 is heading west.

Nene's flying fortress invades Raqueeva. When General Szabo questions Nene about General Logi's activity, Nene tells him to let General Logi handle Shu's group. On the trail of Logi's ship, Shu and Co. end up in battle with the Independent Flying Squadron again. This time, they've all been equipped with Power Boosters to make them more powerful and are instructed to fight them even if it is to the finish. Zola and Marumaro fight Gilliam, Todd, and Bishop while Cynthia and Schneider attack Shu and Co.