Shu and his friends arrive at Jibral Castle, where rumors about ghosts are spreading like wildfire. When a member of Zola's party becomes a prime suspect, the group takes it upon itself to solve the mystery, leading to a confrontation with Salinas, an enemy Shadow wielder.

Shu and the others have finally found Nene. Shu, Jiro, and Marumaro fight Nene while Jiburaru's army is having a hard time fighting Grand Kingdom's army. But then, Shu, Jiro, and Marumaro got to a big disaster and Zola needed to get in.

Homeron informs Shu and Co. about Delphinium who is a Secret Intelligence Agent from Gran Kingdom responsible for the theft of the Extra 7. The group then sees the warships of Sabalu Country (which used to be part of Gran Kingdom) passing. Zola concludes that they give the Sabalu Country airships a warm welcome when the Warship Norg is amongst the Gran Kingdom ships. They managed to obtain one of its Mechats for that action. As the battle starts, they find the Norg and Shu uses Blue Dragon to get Homeron on board. When Kluke lands the ship on the Norg, a fight between the robotic soldiers ensues. Homeron manages to gain some information and prevent the Norg from crashing. He then tries to get info from the ship's captain on where it took Delphinium. When he does squeal that General Logi has the Extra 7, the Norg starts to descend to the ground.

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.

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.

Kluke is shown leaving in a nearby village, being a teacher to some kids and treats the injuries of a boy named Romu after he trips. While at the beach, Bouquet and Marumaro have some fun while Shu goes to the village where Kluke is living. While on the path to the village, Shu runs into Noi who states his interest in finding Kluke and going to awaken her shadow. Meanwhile, Bouquet gets jealous when she hears from Marumaro that Shu went off to look for Kluke. The next day, Kluke leaves to tend to her students. At her house, Shu encounters Andropov who says that Kluke isn't here. Besides stating that he is looking for Kluke, Shu tells Andropov about what happened to Albarose and that General Logi's whereabouts are unknown. Meanwhile, Noi meets with Kluke. Andropov tells Shu that Kluke doesn't want to end up battling again. While the kids are napping, Kluke tells Noi on how she was treating the injured following a great battle and that one of the injured was Andropov. Also when brought up by Andropov to Shu, a flashback depicts Shu telling Kluke that Legolas is organizing a resistance against Rosekstan and states that she doesn't want any part in the resistance. After the flashback, a battle between Shu and Andropove then assume where Shu wins with little trouble due to Andropov's condition. Shu is unable to trample over Kluke and Andropov long found peace causing Shu to leave. Meanwhile, Noi secretly reawakens Kluke's Phoenix without her knowing and departs. Later that evening, Kluke returns home and meets up with Andropov.

As the White Brigade prepares to attack Shu and the others, Shu fends off the White Guardians while Noi evacuates Bouquet and Marumaro away from the area. The White Guardians also retreats as Lotarus watches from afar. Mikhail is shown near a river badly wounded. Shu and Noi have a conversation regarding the events that occurred two years ago as the White Guardians continues their advancement. Later that evening, the village that Shu and Co. are resting turns out to be near the White Guardians' headquarters in the city of Nirvana. Bouquet uses her invisibility to listen out what the White Guardians is up to. Bouquet then unleashes Hippopotamus and takes the form of a White Guardian to throw them off track. Shu and Co. are spotted by some White Guardians, but are knocked out by Saber Tiger. Making their leave from the city, Shu finally encounters Primella in person.

Noi starts to tell everyone about the Investiture Beings' city. At the same time, the Investiture Being leader Rudolph sends Hildegard and Fagino to attack Shu. At the same time, soldiers of the White Guardians train with the Black Shadow Type-Three robots while their Brunacks charge up. When it is charged up, it is fired at the Black Shadow Type-Three robots who lose their shadowy forms. Hildegard and Fagino have arrived on the outskirts of the city. Legolas ends up evacuating the city while the others engage Hildegard and Fagino. Elsewhere, the White Guardians start with their ceremony. Shu, Marumaro, and Bouquet unleash their shadows. Conrad, Griz, and Daner face the two Investiture Beings in unarmed combat. Hildegard uses her wind abilities on them. Back at Nirvana, Primella starts to have visions at the ceremony. While Noi is working on the database, Bouquet and Hippopotamus merge with Blue Dragon while Hildegard and Fagino bring out their dragon forms in their Shadow form. As Hildegard has her dragon use its elasticity on Blue Dragon, Bouquet and Hippopotamus split from Blue Dragon. Hildegard and Fagino counter every move that is thrown at them and managed to take them down. They even managed to detect Bouquet's invisibility as they advance toward the ruins. After destroying the city, Hildegard and Fagino assume their dragon forms and escape. With the ruins also destroyed, Shu's group and Conrad's group go their separate ways.

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.

At a nearby town, Shu has an encounter with Rudolph in the form of a male fortune teller. When in another dimension, Rudolph unleashes winged creatures upon Shu causing him to unleash Blue Dragon. Rudolph also brings out his dragon in Shadow form. Upon managing to pull off an attack on Rudolph, Shu ends up outside of the town as Rudolph unleashes his winged creatures upon it. Shu and Blue Dragon end up fighting them as some of them reach the city. Bouquet and Hippopotamus merge with Saber Tiger to fight off the winged creatures. Noi arrives and merges with Blue Dragon who begins to destroy a lot of the winged creatures. When Rudolph has the winged creatures attacking Marumaro and the Bouquet/Saber Tiger fall back and attack Shu and the Noi/Blue Dragon, the winged creatures ended up destroyed by the Noi/Blue Dragon. Rudolph then leaves after that.

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.