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.

Conrad, Griz, and Daner report what he has found underneath the city to Legolas. Upon remembering what Mikhail said, Noi tells Shu, Bouquet, and Marumaro that he is heading down into the ruins. Noi assumes his dragon form and flies down. While Bouquet and Marumaro have reached a disagreement, Conrad speaks to Shu about what to do with the Investiture Being ruins. Noi manages to get into the database when Lotarus in her dragon form arrives. A flying rock-like structure arrives floating above the city and is a threat if it lands on it. Shu unleashes Blue Dragon and checks it out. Panic occurs in the city as Griz and Daner speak with Bouquet and Marumaro. Blue Dragon attacks the rock structure as Bouquet, Marumaro, and Saber Tiger arrive to help. Bouquet and Hippopotamus merge with Blue Dragon and they attack the floating rock structure. Shu and Blue Dragon use whatever they can to destroy the rock structure and send its debris far. Lotarus takes her leave after this. Later that night, everyone is in the database room. As an eclipse occurs, secret data appears.

Recovering from the fall, Shu is informed by Jiro and Xie about the advancement in the war between the White Guardians and the forces of Rosekstan. Shu then realizes that the village Kluke is living in is right in the middle of the invading forces. Meanwhile, Kluke and Andropov notice one of the Resistance's airships arriving in the village. When they start attacking, Andropov unleashes Alubujem who uses a flash attack to enable his and Kluke's escape. Kluke and Andropov are then pursued by the airship which destroys their house. Riding on a recovered Saber Tiger, Shu, Bouquet, Marumaro and Noi arrive at the ruins of Kluke's house. They then encounter two of the children that Kluke has been educating who tell them everything that has happened. Kluke and Andropov are still on the run from the airship until they crash her hovercycle into a tree. The airship unleashes their armored warriors who bring out their artificial shadows to attack. Andropov unleashes Alubujem to defend himself and Kluke. With some of them defeated, things weren't looking good for Andropov when he gets exhausted. He still tries to defend Kluke even though he has reached his limit. When Andropov is knocked down, Kluke throws herself in front of him as Phoenix is unleashed. As the armored warriors charge toward Kluke and Phoenix, Shu and Blue Dragon arrive in the nick of time taking out some of the the resistance's shadow armours, forcing them to retreat. Upon learning of the current crisis, Kluke and Andropov join up with Shu.

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.

Noi reveals himself to be one of the 'Investiture Beings', but keeps it from Shu and the others to keep their trust. The battle with Shu and Mikhail rages on again with Mikhail unleashing his Red Dragon shadow even when Marumaro and Saber Tiger throw themselves in front of Mikhail's attack. Mikhail reveals his true form as the Red Dragon itself. Meanwhile, Lotarus notices the soldiers in white approaching. The warriors Vermillion and Furioso watch the fight recapping about Primella's prediction of Albarose' destruction when Dr. Tarkovsky appears identifying the Red Dragon as Mikhail as their tri-barrel technological weapons get positioned. Mikhail ends up overpowering Blue Dragon in fusion form. Shu refuses to give up when Mikhail starts attacking Noi for breaking the rules of the Investiture Beings. Then Noi transforms into his black dragon form, revealing himself in front of Shu and initiates the forbidden fusion with Blue Dragon to gain a new dragonite form and evening the odds with Mikhail. During the fight, the soldiers in white step in firing a tri-barrel weapon called the Brunack causing Mikhail to flee. The soldiers corner Shu and co. as Vermillion introduces them as the "White Brigade" and stated that their mission were absolute destructions of all shadows.