Marumaro attacks Shu and the rest, thinking they are responsible for destroying the city. They set a trap and capture Marumaro. After being freed by Zola, Marumaro finds the citizens and Nene's minions. Shu and the rest join the fight and face a pair of twin shadow users. The twins withdraws from the fight and Marumaro joins the team.

Shu and Kluke continue their fight with General Logi and Valkyrie. Marumaro is knocked unconscious by the attacks launched by Schneider's Isabel and Andropov's Alubujem. Luckily, Zola arrives to help Jiro. Meanwhile, Bouquet uses her invisibility to sneak onto Logi's ship and reclaim the Extra 7. Kluke falls unconscious after an attack that broke Valkyrie's shield (whose left wing ends up cut off in the process). The power surge of Blue Dragon's battle with Valkyrie results in a power surge that breaks the glass that's holding the pages. An invisible Bouquet seizes them, but runs into Delphinium who managed to detect her. Logi and Valkyrie managed to bring down Blue Dragon, but Shu gets enraged enough to bring Blue Dragon up to a powerful level. Andropov and Schneider managed to get Logi out of there at the last minute. A debris from the battle makes a hole in the ship as Bouquet manages to make her escape through it only for Delphinium to use her shadow to snatch back the Extra 7 at the last minute. However, Bouquet managed to memorize them enough for her to use Hippopotamus' shape-shifting to turn into copies of them for Shu and Co. to try and decipher.

Shu and Blue Dragon are sent to the nearest town to find a blacksmith to make a replacement part for the Mechat and also to get supplies. On their way to the nearest village, Shu and Blue Dragon save a boy named Tonto from local bandits whose jewels were taken from Tonto. Upon arriving in the village, Shu meets Tonto's sister who happens to be a blacksmith. Shu has some trouble when Tonto steals tomatoes, potatoes, and apples from three local farmers and Shu had to pay for those. Shu and Tonto get into trouble with Tonto's sister when she finds out that Shu is a Shadow Wielder and Tonto had been stealing again. After dodging her hammer before she collapse in sorrow, Shu learns that Tonto's sister hates Shadow Wielders after recurring attack by Shadow Wielders from Gran Kingdom. When asked why Tonto wants to become a Shadow Wielder, Tonto's sister states that Gran Kingdom returned last year with Ivanov and Gustav demanded tribute. Shu and Tonto's sister get word from one of the farmers that the local bandits have captured Tonto. Shu and Tonto's sister managed to find their hideout as the bandits use a tank and robots they stole from Gran Kingdom to attack Shu and Blue Dragon. Due to Tonto's sister not liking Shadow Wielders, Shu is easily taken down by the bandits and Blue Dragon causes them to retreat. After recuperating, Shu finally gets that replacement part for the Mechat and defeats the bandits before rejoining with the others.

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.

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.

Conrad and a Knight Master named Griz join up with resistance headed up by Legolas and Daner in a nearby city and joins him in exploring the ruins of the Investiture Beings there. Shu, Bouquet, Marumaro, and Noi arrive at the city as Lotarus is encountered by Delphinium and Deathroy. Deathroy unleashes Chimera as White Brigade's weapons fire at Lotarus. She manages to evade the weapons and Delphinium's shadow before turning into her dragon form. While Lota deals with Delphinium and Deathroy, she also unleashes winged creatures that attacks the White Guardians. Lota takes the opportunity to escape while Delphinium and the White Guardians are occupied. Shu meets up with Legolas and Conrad and they descend into the underground caverns that are underneath the city. Noi then reads the messages found on the floors of the cavern. When Shu has Blue Dragon punch the artifact on the wall, he is sucked in.

The mysterious person sends Shu's group to a nearby village where they meet up with Jiro and Xie (who first appeared to them as a fruit vendor). Meanwhile at Nirvana, the White Guardians still experiment with their Brunacks on Black Shadows Type-Two with unsuccessful results. Back with Shu and Co., they tell Jiro and Xie what they know about the Investiture Beings. Jiro also informs them that Delphinium is working with the White Guardians and what the White Guardians has been up to recently. They also explain that they've been finding out more about the White Guardians and even interrogated a former member of Gran Kingdom. Meanwhile, General Logi and Matilda flashback to their close call with Lotarus as they view their new giant robots. As the sides of General Logi and Dr. Tarkovsky prepare for battle as the Investiture Beings each watch from a distance, Shu decides to get involved.

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.

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.

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.

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.