Kluke has woken up and is good now. Shu and the others continue their journey to the book of origins. Now Shu and the others are in logic city in their journey.

Cynthia has grown jealous of Bouquet's beauty. This causes her to seek out and eliminate her. A fight on the narrow path causes everyone to fall into Death Valley. Bouquet brings out her Hippopotamus shadow to turn into a ball...which ends up scattering everyone. As Shu and Co. evade the experimented creatures there, Cynthia learns from Andropov that the fog there has softened the cliff sides to the point where it is impossible to climb. As Andropov tries to find a way out for Cynthia, Bouquet and Hippopotamus secretly follow her to find a way out with Bouquet leaving a trail of her clothes for the others to follow. When her cover ends up blown near the exit of Death Valley, Cynthia attacks. Things weren't looking good for Bouquet and Hippopotamus. When Shu and Co. arrive, Cynthia retreats.

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.

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.

Kluke starts to get exhausted from various teleporting when getting some White Guardian soldiers away from the battle. After decimating half of the White Guardians' troops, General Logi clashes with Furioso. As the battle rages on, the Investiture Beings continue their meeting as Mikhail plans to take action upon both sides despite the objections of Hildegard and Lotarus. Shu and the Noi/Blue Dragon have begun their fight with Vermillion. Kluke finally collapses from the strain. Meanwhile, Delphinium and Matilda engage each other in battle which ends with Matilda having Zephyrus teleport her away from Delphinium and Deathroy. As Shu and Vermillion are locked in combat, Mikhail ends up leaving the floating city. General Logi and Furioso are still locked in combat until Furioso leads him into a trap consisting of the White Guardian soldiers firing their cannons at him. General Logi manages to evade it and makes a striking blow toward Furioso only for one of the White Guardian soldiers to throw himself in front of Furioso. Jiro and Xie continue their reconnaissance. General Logi's hideout blows up to reveal a weapon air fortress called Sleipnir which decimates some of the Brunacks. During Shu's fight with Vermillion, Mikhail arrives and assumes his Red Dragon form and starts attacking the Rosekstan soldiers and the White Guardian soldiers. Shu and the Noi/Blue Dragon managed to put up a barrier to protect Jiro and Xie. Shu ends up going into overdrive which starts to make the grounds unstable, but lets himself get beat due to the pleas of Kluke, Bouquet, and Marumaro.

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.

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.