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.

Shu and the others manage to protect the village from the enemy. The ‘Knight Master’ (Zola) convinces Shu to come along on their journey.

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 finds the gang and and now is in the Grand Kingdom's capital city. While that, Grand Kingdom's army is fighting Jiburaro Kingdom's army. Shu Nand the others get inside Nene's place(nene is a villain). While Shu and the others are finding Nene, they discover that Nene is planning to take out children's shadows and using them as their weapons.

Shu's informant Homeron is gathering information about the Extra Seven. Shu and Co. arrive at Flame Phoenix ruins. When Kluke disappears, she ends up in the area where she first encountered her Phoenix shadow and asks it how she can call upon its power again. Phoenix tells Kluke that the answers lie in herself. Kluke then receives a necklace and rejoins Shu and Co. When they find Jibral's scattered army being attacked, Shu and Co. join the battle. Upon defeating the robotic soldiers and their shadows, Shu and Co. are soon attacked by a giant robot. Kluke brings out her Phoenix Shadow to use its barrier to protect everyone enough for Shu to use Blue Dragon to destroy the giant robot. Meanwhile, Homeron receives news the mysterious woman who stole the Extra 7 is heading west.

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.

Nene's flying fortress invades Raqueeva. When General Szabo questions Nene about General Logi's activity, Nene tells him to let General Logi handle Shu's group. On the trail of Logi's ship, Shu and Co. end up in battle with the Independent Flying Squadron again. This time, they've all been equipped with Power Boosters to make them more powerful and are instructed to fight them even if it is to the finish. Zola and Marumaro fight Gilliam, Todd, and Bishop while Cynthia and Schneider attack Shu and Co.

The battle against Logi's Independent Flying Squadron rages on as Shu, Kluke, Jiro, and Bouquet struggle to take down Cynthia while Zola and Marumaro do the same for Gilliam and his minions. When Marumaro takes down Bishop, he and Zola focus on the remaining two when Gilliam and Todd's Power Boosters overload. When this is discovered, General Logi orders Cynthia, Gilliam, and Todd to retreat, but Gilliam and Todd are shot down by Zola after Marumaro decoyed them. Despite Cynthia going into overdrive, she is defeated by Jiro anyway.

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 breaks Valkyrie's shield. The Blue Dragon's battle with Valkyrie breaks the glass that's holding the pages. An invisible Bouquet seizes them but runs into Delphinium. Logi and Valkyrie manage to bring down Blue Dragon, but Shu gets enraged enough to bring Blue Dragon up to a powerful level. Andropov and Schneider manage to get Logi out of there at the last minute. 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.

Gilliam is recuperating at Castle Des La Teste and recovers quickly in a plot to take revenge on Zola. Delphinium allows Gilliam to take the type-three models of the Black Shadow robots with him. Kluke and Bouquet argue where to go next when Zola tells them that they have to refuel the Mechat. Meanwhile, Nene is informed that the drilling beam on his flying fortress is almost up to power. While Shu and Jiro protect Kluke while she refuels the Mechat, Zola and Marumaro take on the soldiers positioned there. Gilliam receives word from Delphinium that the Gran Kingdom strategic refueling base was attacked. Kluke is told by Zola to head to the Hippopotamus Ruins since Nene's flying fortress is heading there. Gilliam attacks and Zola engages him while the others fight his Black Shadows. Kluke solves Chapter Seven of the Extra Seven and uses the crystal on her necklace to power up Phoenix when the Black Shadows charge up their attack.

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.

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.

Recovering from the fall, Shu is informed by Jiro and Xie about the advancement in the war between the White Guardians and the forces of Rosekstan. Shu then realizes that the village Kluke is living in is right in the middle of the invading forces. Meanwhile, Kluke and Andropov notice one of the Resistance's airships arriving in the village. When they start attacking, Andropov unleashes Alubujem who uses a flash attack to enable his and Kluke's escape. Kluke and Andropov are then pursued by the airship which destroys their house. Riding on a recovered Saber Tiger, Shu, Bouquet, Marumaro and Noi arrive at the ruins of Kluke's house. They then encounter two of the children that Kluke has been educating who tell them everything that has happened. Kluke and Andropov are still on the run from the airship until they crash her hovercycle into a tree. The airship unleashes their armored warriors who bring out their artificial shadows to attack. Andropov unleashes Alubujem to defend himself and Kluke. With some of them defeated, things weren't looking good for Andropov when he gets exhausted. He still tries to defend Kluke even though he has reached his limit. When Andropov is knocked down, Kluke throws herself in front of him as Phoenix is unleashed. As the armored warriors charge toward Kluke and Phoenix, Shu and Blue Dragon arrive in the nick of time taking out some of the the resistance's shadow armours, forcing them to retreat. Upon learning of the current crisis, Kluke and Andropov join up with Shu.

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.

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.

Rudolph recalls Hildegard and Fagino to his castle when the Mast Driver approaches their realm. As the Mast Driver approaches the area, strange aircraft attack. From within their ship, Shu and Marumaro send Blue Dragon and Saber Tiger out to fight them. With help from Noi, Blue Dragon and Saber Tiger trick the aircraft into crashing into each other. They finally arrive at the Investiture Beings' castle. Fagino is sent to attack them and unleashes his shadow. The other Investiture Beings watch from their castle.

Shu continues his fight with Rudolph. After taking a blow from Blue Dragon, Rudolph assumes his dragon form. Rudolph and the Shu/Blue Dragon are easily matched until Rudolph manages to strangle him. He repels Noi and the Bouquet/Saber Tiger. When Rudolph starts to finish off the Shu/Blue Dragon, Noi unleashes his power which enables his dragon form to get bigger. With this occurrence, Noi engages Rudolph. Both of them are easily matched. Right when Rudolph was about to finish off Noi, he is hit by an attack launched by the Shu/Blue Dragon. Rudolph enters a portal that he created and the Shu/Blue Dragon follows him into it. The Shu/Blue Dragon follows Rudolph into an area where he uses a war machine to defeat the Shu/Blue Dragon. The Investiture Beings' castle is starting to change shape into a large dragon-like war machine. Kluke uses her forcefield ability to protect them from its attack. Just then, Rosekstan's forces arrive as Shu's unconscious body is approached by Primella.

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.

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.