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 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.

When Nene's fortress starts attacking Coreed, Conrad has Shu and Co. ride giant birds called Gryphs to Nene's fortress while Conrad and the others fight Black Shadow Type-Two robots. Zola also tells Shu and the others that Nene is one of the descendants of the Soldiers of Light. They successfully infiltrate the fortress. Once inside, they end up in the S-Field and fight Black Shadow Type-Three robots which have nanobot technology that enables them to regenerate. After recurring take downs on the Black Shadows, Bouquet and Hippopotamus manage to find the control room General Szabo is in and gets in as Nene. Bouquet then reveals herself and then transforms into a Black Shadow Type-Three and manages to use Hippopotamus' new ability to copy the optic attack of the Black Shadow Type-Three which sends General Szabo flying into the air and exploding. After Bouquet shuts down the Black Shadows, Shu and the others locate Nene's throne room for the final battle.

The mysterious woman before now known to be named Lotarus is shown to be one of seven shadowy dragon from the castle in the sky. She is given freedom to re-judge the people of the world even after her ordeal with Logi. She runs into Mikhail and tells him that she will handle the next test. In Logic, Shu is at the library looking up while Bouquet takes Marumaro and Noi out shopping for groceries. After Marumaro and Noi ditch Bouquet, she runs into Lotarus (who uses the alias of Lota) who becomes curious about her. She asks what Bouquet wished for if she had power, but she replies that she already has everything she wants. Meanwhile, Shu finds nothing on where the dragon sightings are. Bouquet finishes her shopping with Lotarus and takes her around town. Shu is still trying to find the sightings of the Red Dragon on the map while recapping what Mikhail said. While Marumaro and Noi are enjoying an ice cream cone, Noi ends up noticing Lotarus near Bouquet. Noi runs off to tell Shu that Bouquet might be in danger. Shu even recaps about Xie telling him about a woman floating over the waters when Albarose was destroyed. While in the park, Lotarus forges a Dragon Scale Pendant behind her back and begins to offer it to Bouquet stating that it will give Bouquet what she wishes for. But before Bouquet can accept Lotarus' gift, Shu cuts in and identifies Lotarus as being in the same race as Mikhail. As Shu unleashes Blue Dragon, Lotarus ends up unleashing her shadow that resembles a white dragon with pink wings. Shu and Blue Dragon fight Lotarus as she states about the Dragon Scale tests causing Shu to recap the incidents with Crester and the moving pyramid. Lotarus states that the Dragon Scale tests were done by Mikhail and that Mikhail had been watching him. Right when Shu and Lotarus are about to make their next move, Bouquet interferes causing the match to be a draw. Before she departs, she tell Shu and Bouqet to tell Noi to make his decision as well. Later that evening, Shu gets Marumaro and tells them that they are going to find Mikhail who is spotted nearby the wetlands at the edge of Logic.

Noi starts to tell everyone about the Investiture Beings' city. At the same time, the Investiture Being leader Rudolph sends Hildegard and Fagino to attack Shu. At the same time, soldiers of the White Guardians train with the Black Shadow Type-Three robots while their Brunacks charge up. When it is charged up, it is fired at the Black Shadow Type-Three robots who lose their shadowy forms. Hildegard and Fagino have arrived on the outskirts of the city. Legolas ends up evacuating the city while the others engage Hildegard and Fagino. Elsewhere, the White Guardians start with their ceremony. Shu, Marumaro, and Bouquet unleash their shadows. Conrad, Griz, and Daner face the two Investiture Beings in unarmed combat. Hildegard uses her wind abilities on them. Back at Nirvana, Primella starts to have visions at the ceremony. While Noi is working on the database, Bouquet and Hippopotamus merge with Blue Dragon while Hildegard and Fagino bring out their dragon forms in their Shadow form. As Hildegard has her dragon use its elasticity on Blue Dragon, Bouquet and Hippopotamus split from Blue Dragon. Hildegard and Fagino counter every move that is thrown at them and managed to take them down. They even managed to detect Bouquet's invisibility as they advance toward the ruins. After destroying the city, Hildegard and Fagino assume their dragon forms and escape. With the ruins also destroyed, Shu's group and Conrad's group go their separate ways.