The final battle arrives between Shu and the more powerful demon Zola. After Shu defeats Zola everyone begins the resealing of the darkness. But they learn that in order to free the world of darkness, a sacrifice of the shadows must be made. So everybody uses up every last drop of energy that their shadows possess and they reseal the darkness. The world returns to normal, and everyone resumes their normal lives.

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.

Arriving to Coreed, Shu, Bouquet, Marumaro, and Noi ask Homeron the Original to help them in locating Jiro, but learn that he has retired and recommends one more skilled than he is. Upon learning the triangular pattern as part of Homeron the Original's riddle about someone inheriting Homeron's wishes, they end up at the house of Xie (the girl that Homeron the Great was disguised as in an earlier encounter). Before getting down to business, she informs the group that Rosekstan's capital Albarose was destroyed throwing the world in chaos. Xie also mentions that the Red Dragon that Shu had encountered happens to be sighted whenever coup d'état, wars, and natural disasters are going to occur. She does managed to give them directions on where Jiro and Kluke are residing.

Meanwhile, Jiro has a run-in with Delphinium and Deathroy which ends with Delphinium escaping. When Shu, Bouquet, Marumaro, and Noi arrive at Jiro's training hut. Jiro declines Noi's offer to regaining his shadow and rejoining Shu's group. Shu goes against Jiro to see what he has learned, when fighting Blue Dragon. After Jiro managed to knock down Shu, Jiro tells he was training hard in the last 2 years so that he can one day defeat Delphinium. Eavesdropping about Noi's abilities, Delphinium attacks and captures Bouquet. She uses her as a "trade card" to get Noi to reawaken Deathroy's shadow Chimera. Noi does so and preforms the Tosen Kyuden ability on Deathroy which reawakens Chimera. After the events, Jiro and Shu's party begins traveling in their different paths with Jiro in pursuit of Delphinium and reunite with Minotaur in later time.

After Shu's brief talk with Primella, Noi finds a path out of Nirvana while Shu options another route for their next destination. Shu and Co. make their way through the city while evading the White Brigade's patrolling shifts commandeered by Furioso's intelligent tactics. During this part, Bouquet's hair touching Marumaro's nose causes him to sneeze giving them away to one of the security shifts. Shu and Marumaro manage to take them down as the next shift appears. Lucky for them before the soldiers ca signal, Jiro arrived and took them down. Jiro manages to create a diversion as Shu and the others make their escape, but Furioso easily recognises the ruse. When Furioso gets ready to intercept and fire where Shu and Co. are, Dr. Tarkovsky intervenes and tells him and the soldiers in the area to fall back, courtesy of Primella's plea.

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.

At Nirvana, Vermillion and Furioso are overseeing the upgrades to their weapons and rethink of what had happened in their fight with Rosekstan. Vermillion later reviews about recent events with Dr. Tarkovsky which is overheard by Delphinium and Deathroy. Furioso has a new sword made and trains with his fellow soldiers. Vermillion later joins the practice and nearly bests Furioso. A flashback showed how Vermillion fought against Gran Kingdom when Nene was in power and how Vermillion joined up with Dr. Tarkovsky.

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.

Things aren't looking good for Rosekstan and Shu's allies. Just then, the Shu/Blue Dragon emerges with Primella in its hand. Primella wakes up as she is given to Dr. Tarkovsky and General Szabo. Rudolph emerges from the war machine and fights the Shu/Blue Dragon. They match blow to blow until Rudolph uses his intangibility to keep the Shu/Blue Dragon from hitting him and then multiplies to attack the Shu/Blue Dragon. With help from Primella, the Shu/Blue Dragon destroys the duplicates. The Shu/Blue Dragon collides its punch with Rudolph's punch. The hopes of Shu's allies, Marumaro's siblings, and even the thought-dead Conrad, Griz, and Daner help give the Shu/Blue Dragon the strength to fight Rudolph. Their combined attacks results in an explosion that destroys the winged creatures and the dragons that Rudolph had summoned. As the Shu/Blue Dragon falls to the ground, Rudolph starts to crack up and explode taking his war machine with him.