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

During the battle with the Grankingdom, seven pages from the "Book of the Beginning" were stolen--pages with key information about Shadow powers. Zola's group decides to make for the Grankingdom, and head out to sea--with Bouquet on board as an unexpected stowaway. When a suspicious fog rolls in, and Shu and his friends are overcome with mysterious symptoms, it's up to Bouquet to save the day...

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.

Shu and Co. encounter Homeron again. He reveals that the information of the Extra 7 is somewhere in Gran Kingdom's Castle Des La Teste and they will have to infiltrate it to get to its master computer. Conrad L. Lawrence is shown to be imprisoned in a local prison run by Cynthia which Homeron also tells Shu. Zola comes up with a plan to lure the guards from Castle Des La Teste in order to rescue Conrad and get the information. As the others attack the prison, Homeron, Kluke, and Bouquet infiltrate the castle. Upon rescuing the captive soldiers, Shu and Jiro free Conrad and run into Cynthia. Lemaire also arrives to help Cynthia and both of them begin to overwhelm Shu and Jiro until a successful attack from Blue Dragon and Minotaur weakens them down. Zola catches up after destroying the robots that came with Lemaire. With the reinforcements from Castle Des La Teste approaching, Zola issues a retreat as Homeron begins his infiltration.

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.

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.

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.