Shu and the others have finally found Nene. Shu, Jiro, and Marumaro fight Nene while Jiburaru's army is having a hard time fighting Grand Kingdom's army. But then, Shu, Jiro, and Marumaro got to a big disaster and Zola needed to get in.

Marumaro finds himself in hot water when he flirts with the innkeeper's wife, and he's in even deeper trouble when it turns out the inkeeper is a Shadow Wielder who deserted Gran Kingdom's army with the "wife" being his shadow. They soon learn that Marumaro isn't from Gran Kingdom. Marumaro and Saber Tiger later defend them from a Gran Kingdom captain and his troops with the innkeeper on his bounty list. Marumaro and Saber Tiger defeat them and they reunite with Shu and the others.

Cynthia has grown jealous of Bouquet's beauty. This causes her to seek out and eliminate her. A fight on the narrow path causes everyone to fall into Death Valley. Bouquet brings out her Hippopotamus shadow to turn into a ball...which ends up scattering everyone. As Shu and Co. evade the experimented creatures there, Cynthia learns from Andropov that the fog there has softened the cliff sides to the point where it is impossible to climb. As Andropov tries to find a way out for Cynthia, Bouquet and Hippopotamus secretly follow her to find a way out with Bouquet leaving a trail of her clothes for the others to follow. When her cover ends up blown near the exit of Death Valley, Cynthia attacks. Things weren't looking good for Bouquet and Hippopotamus. When Shu and Co. arrive, Cynthia retreats.

Shu and Blue Dragon are sent to the nearest town to find a blacksmith to make a replacement part for the Mechat and also to get supplies. On their way to the nearest village, Shu and Blue Dragon save a boy named Tonto from local bandits whose jewels were taken from Tonto. Upon arriving in the village, Shu meets Tonto's sister who happens to be a blacksmith. Shu has some trouble when Tonto steals tomatoes, potatoes, and apples from three local farmers and Shu had to pay for those. Shu and Tonto get into trouble with Tonto's sister when she finds out that Shu is a Shadow Wielder and Tonto had been stealing again. After dodging her hammer before she collapse in sorrow, Shu learns that Tonto's sister hates Shadow Wielders after recurring attack by Shadow Wielders from Gran Kingdom. When asked why Tonto wants to become a Shadow Wielder, Tonto's sister states that Gran Kingdom returned last year with Ivanov and Gustav demanded tribute. Shu and Tonto's sister get word from one of the farmers that the local bandits have captured Tonto. Shu and Tonto's sister managed to find their hideout as the bandits use a tank and robots they stole from Gran Kingdom to attack Shu and Blue Dragon. Due to Tonto's sister not liking Shadow Wielders, Shu is easily taken down by the bandits and Blue Dragon causes them to retreat. After recuperating, Shu finally gets that replacement part for the Mechat and defeats the bandits before rejoining with the others.

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.

Shu's party crosses the desert to find a huge pyramid and right across was Heliut, a town with many casinos. In the town, they find Legolas, their leader of the resistance who came to Heliut to procure enough funds for his resistance by going to the casinos. He ended up to his life in debt to Mayor Heliut the IV after Legolas lost it. It was during the conversation suddenly, the pyramid began to rise and starting moving towards the town launching its bricks toward Heliut. The armies of Mayor Heliut the IV fail to stop it. Attempting to settle his debt by saving Heliut, Legolas sends Shu's party to demolish the pyramid after speaking to Mayor Heliut the IV. Bouquet and Hippopotamus merge with Shu's Blue Dragon as Marumaro unleashes Saber Tiger. Every attack that the Bouquet/Blue Dragon does to the pyramid, it rebuilds itself. Mayor Heliut the IV tells Legolas that if anything happens to his city, he will hold Legolas responsible. Noi comes with a plan which involves Bouquet splitting from Blue Dragon and merging with Saber Tiger. When the Bouquet/Saber Tiger gets close, Shu has Blue Dragon attack followed by the Bouquet/Saber Tiger attacking the core. When they managed to stop the pyramid, they discover that one of Mikhail's Dragon Scales was placed in a mummy. After being congratulated by Mayor Heliut the IV, the group learns that Legolas' deal to him was that they would stop the pyramid in exchange for being free from his debt. While Shu angrily chases after Legolas, Bouquet, Marumaro, and Noi enjoy their stay in Heliut.

In a broken-down village, Shu's party encounters a girl named Linda who tells them that the Brigands consisting of Schmidt and his army of Mecha Robos (which were salvaged from the war) keep attacking her village to steal everything. Linda reveals that the villagers shun conflict to evade standing up to Schmidt. When the villagers return. It is here that Noi met his first love in Linda. Shu, Bouquet, Marumaro, and Noi help the villagers rebuild their village. After some romantic hintings by Marumaro to Noi, Schmidt and his army of Mecha Robos arrive and attack the village. While Noi and Linda evacuate the village, Shu, Bouquet, and Marumaro holds off the Mecha Robo army. After the villagers are safely in the mountains, Shu and Marumaro unleash their shadows and fight back. Meanwhile, Schmidt finds the hiding place of the villagers and finds their hidden treasure while the Mecha Robos with him restrain the villagers. When it comes to protecting Linda and the villagers, Noi reveals himself to be the young black dragon (from episode one) when trying to save Linda. Noi in his dragon form then attacks the Mecha Robos. Meanwhile, Shu and Marumaro finish off the Mecha Robos in the village. After taking out the Mecha Robos, Noi engages Schmidt in battle and defeats him. Upon seeing Linda's reactions, Noi flies off as Shu, Bouquet, and Marumaro catch up to the villagers. Moments later, the villagers rebuild their village as Shu, Bouquet, and Marumaro wonder how Schmidt was taken down as Noi returns. As they leave, Linda appears to say goodbye to Noi.