The battle against Logi's Independent Flying Squadron rages on as Shu, Kluke, Jiro, and Bouquet struggle to take down Cynthia while Zola and Marumaro do the same for Gilliam and his minions. When Marumaro takes down Bishop, he and Zola focus on the remaining two when Gilliam and Todd's Power Boosters overload. When this is discovered, General Logi orders Cynthia, Gilliam, and Todd to retreat, but Gilliam and Todd are shot down by Zola after Marumaro decoyed them. Despite Cynthia going into overdrive, she is defeated by Jiro anyway.

Zola has been defeated while Marumaro and Saber Tiger free Kluke, Phoenix, Bouquet, and Hippopotamus. Shu and Jiro have Blue Dragon and Minotaur attack Nene. Nene combines the Chimera clones to form one large Chimera. Meanwhile, General Logi has dispatched his troops which will attack when Schneider and Andropov receive the command from General Logi. Nene uses Chimera's Dark Symphony attack which weakens his opponents. When Shu and Blue Dragon's attacks are countered by Chimera's attack, Shu falls unconscious. In a dream sequence, he encounters Lt. Dragnov and Homeron. Marumaro and Kluke are defeated as Jiro has Minotaur aim for the device on Chimera's forehead. Shu rises from his boulder grave for another bout with Nene. Assisting Jiro and Minotaur in attacking the crystal on Chimera's forehead, Shu and Blue Dragon learn that the crystal enabled Chimera to alter his elements. The limiter is unleashed as Nene and Deathroy merge with Chimera to form an amalgam of all three of them. With Jiro defeated, Shu uses every ounce of his power and manages to destroy Nene as Deathroy is shown lying on the ground. With news of Nene's defeat, General Logi gives the command and has Schneider take over Castle Des La Teste while Andropov attacks some Gran Kingdom airships. This is General Logi's act of his secession from Gran Kingdom which he announces.

At a Rosekstan base, General Logi oversees the upgrades to the giant exo-suits while on Sleipnir, Matilda is given the status on the giant wall. Rosekstan's forces still try to breach the wall as Shu, Bouquet, Marumaro, and Noi arrive at the nearest village. Matilda resolves to use a powerful laser that would guarantee the wall's destruction at the price of the nearest village. As Saber Tiger is riding the others toward the giant wall, they are ambushed by Matilda and the exo-suit warriors. Not wanting Matilda's plan to happen, Shu unleashes Blue Dragon as Matilda unleashes Zephyrus.

In a stormy volcanic area, Noi runs into Legolas nearby Z'Mey: a dragon sanctuary. Conrad also arrives with Griz and Daner. Meanwhile, Marumaro and Bouquet continue their search for Kluke. At a nearby town, Kluke is shown tending to the injured. Daner shows Noi an artifact that Conrad's group had found. Noi then leads Legolas, Conrad, Griz and Daner into Z'Mey and go through many obstacles to get to the main chamber. Meanwhile, Shu sees a nearby town that is annihilated when Rudolph arrives. Shu and Rudolph unleash their shadows and fight. Noi places the artifact in the area and it unveiling a shuttle called Mast Driver and its pyramid-like platform. The light it emits is noticed by Shu and Rudolph as Rudolph leaves. Meanwhile, Bouquet and Marumaro have met up with Kluke at the area where Primella's vision of her took place.

The battle between Rudolph and the Shu/Blue Dragon begins. Rudolph's shadow is matching blows with the Shu/Blue Dragon and nearly defeated Marumaro and the Bouquet/Saber Tiger. Rudolph starts to overwhelm the Shu/Blue Dragon. When Rudolph overwhelms the Shu/Blue Dragon sending him into a ditch with Primella and Dr. Tarkovsky falling after him. The attack also defeats Marumaro and the Bouquet/Hippopotamus. Noi even tries to have some words with Rudolph. Primella continues to glow and makes contact with Shu mentioning how she was a part of Zola before being separated from her by Killer Bat. After the talk, the Shu/Blue Dragon rises to continue his fight with Rudolph. Noi assumes his dragon form and tries to fight Rudolph, but to no avail. Before Rudolph can finish Noi off, the Shu/Blue Dragon saves him. Bouquet re-merges with Saber Tiger to assist Shu in the fight with Rudolph.

Rosekstan begins their attack on Rudolph's war machine. Rudolph then unleashes his winged creatures, a bunch of Amethyst Dragons, a Moody Dragon, and a Phantom Dragon. Jiro, Kluke, Marumaro, Bouquet, Andropov, and General Logi unleash their shadows to attack the war machine while Noi looks for Shu. Meanwhile, Shu makes contact with Zola's spirit. As the battle progresses, Rudolph's war machine decimates most of the Rosekstan fleet. Just as one of the winged creatures is about to attack Jiro, he is saved by Delphinium and Deathroy (who have unleashed Chimera) as they arrive with reinforcements. Sleipnir fires its cannon at Rudolph's war machine but to no avail. Rudolph then fires the attack which decimates more Rosekstan airships as Noi charges towards the war machine.