A boy named Shu is obsessed with knight masters learns that one has appeared in his village. Shu gets excited at this possibility and goes in search of him. His village gets attacked after finding the "knight master". Shu unleashes his true power after finding his friends are in trouble.

Zola and the team assault the fortress to free the captives from the city. Logi defeats Zola, then defeats both Jiro and Marumaro. He leaves for an audience with Nene, leaving the twins in charge. Shu manages to manifest and control the Blue Dragon, defeating the twins in the process. Shu and the rest then receive a mission to escort Legolas to the capital.

Shu and his friends want to hire an informant to help them find the Extra Seven but are told that an informant named Homeron the Great had died in battle against Gran Kingdom. At the same time, they meet the other Homerons ranging from Homeron the Original, Homeron II, Homeron the Legitimate, and Homeron Jr.. To pay for another informant, Shu heads off on his own to defeat the dangerous monster called the Gigarus and claim the reward. Shu and Blue Dragon managed to defeat the Gigarus and the group learns that the woman that hired Shu is actually Homeron the Great. However, Marumaro has gotten lost from the group.

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.

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.

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.

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.

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.