Zola and company meets the king who grants her access to the ancient library. Shu finally meets a true knight master. Bouquet arrives at the city to find it under attack from Nene's robotic shadow users. Shu and company joins the fight. An ancient scroll is stolen in the chaos and given to a mysterious character.

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.

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.

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.

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.