It has been two years since the battle with Darkness. Shu has since lost Blue Dragon. Along with Bouquet and Legalas, Shu has formed a resistance group that is fighting Rosekstan.
Even after his escape from a giant Red Dragon, Nöe won't reveal anything, no matter what he is asked. Shu, Bouquet and Nöe set out on a journey to see Marumaro.
Shu and his friends join with Marumaro and head off to Korin, in order to gather information on their other friends. They come across a mountainous region that is being attacked by the Rosekstan army.
Shu and his friends are on their way to Korin. The group stops by Harrywood, a gorgeous city built near a pyramid. There they find Legalas, who is wearing a bunny outfit.
While traveling, Shu and his friends come across a run-down town. The town is now trying to rebuild itself after being attacked by a robot bandit gang led by Schmitt.
Shu is in the library by himself, worrying about how he can obtain information about the enemy. Bouquet goes out shopping to cook for Shu and bumps into Rottarace.
Shu and his friends are on their way to Korin. The group stops by Harrywood, a gorgeous city built near a pyramid. There they find Legalas, who is wearing a bunny outfit.
Along their way, Shu and his friends help a girl who is pulling a heavy cart. The girl treats them to a meal in return for their help. They fill their stomachs.
Shu and the team find out that the fate of their world depends on their decisions. Furthermore, Bouquet and Marumaro are not sure of what to do when they are told that many of their actions were mistakes.
Shu and his friends learn that other temples exist other than the one in Buoyla. They suspect that they can extract information about their enemy's stronghold.
Shu and his friends have run out of traveling money and go to a local bakery in search for a job, where they are given a test by the sisters who run the shop.
Along the way, Marumaro falls in love at first sight with a beautiful noblewoman. The group tries to control Marumaro's frenzy as they visit a nearby town, but something is wrong.
Shu and his friends gather in town after being contacted by Sui, an informant. There they are reunited with Jiro, who is traveling with Sui since their escape from Nirvana.
Shu and his friends receive help from Kluke and arrive in the Galleon. Logi agrees to talk and Shu asks him to stop the war, but Logi immediately refuses.
The war between Rosekstan and the White Guardians begins. But Shu doesn't stop trying to reduce the war's casualties. Kluke and the others meet up with him.
The war reaches a climax and Shu takes on Vermillion one on one. They discuss each other's points of view and Vermillion tells Shu that he thinks that Shu is trying to kill Purimura.
Mikhail has come to destroy humans by himself. But Rudolph, the leader of the Legion of Elite Species, creates a giant wall to punish Mikhail for his actions.
The White Guardians come back from to Nirvana. Purimura says that fate is something that must be accepted. Her heart aches over the loss of all the lives during the war.
Shu and the team visit the Utopian town of Moa in order to take on Hildegard's trials. There, the town representative, Junger, as well as the other townspeople, greet them with smiles.
The Legion of Elite Speices watched the results of the trail that Shu was given to by Rudolph. They finally begin their final discussion about the human race.
Shu and his friends struggle to protect people from the attacks of the Legion of Elite Species. Purimura, who is accompanied by Vermillion, receives a premonition that a White Dragon will stab Kluke.
Shu and his friends are saved by Vermillion's life-risking actions. In order to prevent his desire of overcoming fate from going to waste, Nöe heads to Zmey and Bouquet and Marumaro set off to save Kluke.
Jiro and Sui are caught for spying in a base where Logi is developing new weapons. While the two of them look for a chance to escape, Hildegard appears leading the Sky Dragons.
Shu's group has been split into three and are all headed to their destinations. Nöe reaches Zmey, but the Legion of Elite Species has already destroyed it.
Relying on the words of the Oracle, Bouquet and Marumaro are reunited with Kluke. Places with flowers are dangerous, so the two force Kluke to escape with them into the town.
Shu is with Purimura. He comes into contact with the White Guardians. He asks Doctor Tarkovsky to help him in his battle against the Legion of Elite Species. But Doctor Tarkovsky turns him down.
Shu gains the cooperation of the White Guardians. They gather in Zmey along with Bouquet and the others, who saved Kluke. In Zmey, Nöe is fine-tuning the ship that will take them to the sky.
Shu and the others defend the Massdriver from attacks from the Sky Dragon. These new enemies place them in a predicament. They don't give up hope and continue to fight.
Shu and the others vow to defeat Rudolph. The Legion of Elite Species' defense system attacks their ship. Shu and Marumaro retaliate with their shadows, but they struggle because of the sheer numbers of their enemies.
As Shu and the others go to fight Rudolph, Forgino stands in their way. In order to fight the Legion of Elite Species, Shu tries to "Merge" with Blue Dragon, but fails. Blue Dragon is unable to move.
Shu and the others see Rottarace being put on trial. As everyone is unsure of what to do, Purimura tells Shu that they should save her. Upon hearing this, Doctor Tarkovsky objects, saying that they cannot risk falling into an enemy's trap.
Rudolph reveals his true goal. He wanted to collect data on all of the incomprehensible actions that Shu and the others took during his trials. He needs the information to help the Legion of Elite Species thrive.
Shu and Blue Dragon fight Rudolph with the help of their friends. Nöe and Marumaro stand no chance against Rudolph. Rudolph goes one-on-one against Blue Dragon.
Shu is left behind in Castle Azure. Jiro and the others try to save him. But they cannot approach the castle because of a powerful barrier. Countless dragons are released and attack the group.
