Logi and the others ran away from Shu and the gang. After the fight Shu and the others got separated accidentally, but the commander, Rogi, and the others will be planning to surprise Shu and the gang again. Logi and the others are trying to find each other.

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.

Homeron informs Shu and Co. about Delphinium who is a Secret Intelligence Agent from Gran Kingdom responsible for the theft of the Extra 7. The group then sees the warships of Sabalu Country (which used to be part of Gran Kingdom) passing. Zola concludes that they give the Sabalu Country airships a warm welcome when the Warship Norg is amongst the Gran Kingdom ships. They managed to obtain one of its Mechats for that action. As the battle starts, they find the Norg and Shu uses Blue Dragon to get Homeron on board. When Kluke lands the ship on the Norg, a fight between the robotic soldiers ensues. Homeron manages to gain some information and prevent the Norg from crashing. He then tries to get info from the ship's captain on where it took Delphinium. When he does squeal that General Logi has the Extra 7, the Norg starts to descend to the ground.

Following the trail of the downed Norg ship, Shu and Co. look for Homeron and the Norg's crew in the Great Brandish Forest which is on the border of Gran Kingdom and Sabalu Country. Delphinium is also in the woods searching for the Norg Crew. Shu, Jiro, and Marumaro as well as Homeron and the Norg Crew are soon attacked by Obacks (one-eyed single-horned bears (known as Horned Lazy Bears within the Blue Dragon Game for the Xbox 360)). Even when Shu catches up with Honmalon at where the Obacks nest, Delphinium arrives and uses her shadow to kill Homeron. After evading Blue Dragon, Delphinium escapes. With the crew of the Norg freed, the captain of the Norg tells Shu that the Extra Seven are on General Logi's ship.

During their search for Jiro, Shu runs across news of a small war about to happen between a Rosekstan sub fleet led by Captain Varenko and a small band of resistance led by Captain Crester (one of the surviving members of Grand Kingdom). The party continues forward anyway hoping not to get found, leading to the combination of Saber Tiger and Hippopotamus with the 'stealth mode'. During but a few moments, Crester's band of resistance were eliminated. It was then suddenly Micheal appears before Crester and grant him the power to call his own Wyvern-like shadow allowing him to devastate General Logi's sub fleet. Having found out that the shadow that Crester wields is different from the normal Shadows and the Artificial Shadows used by Grand Kingdom, Shu's party steps in to defeat Crester. After defeating Saber Tiger and Hippopotamus, Crester faces off against Shu and Blue Dragon. After Crester is defeated, Shu, Bouquet, and Marumaro learn about the 'Dragon scales' Mikhail handed out which can grant miraculous powers to the user. They then overhear one of the Rosekstan soldiers tell Captain Varenko that they lost contact with General Logi.

Kluke is shown leaving in a nearby village, being a teacher to some kids and treats the injuries of a boy named Romu after he trips. While at the beach, Bouquet and Marumaro have some fun while Shu goes to the village where Kluke is living. While on the path to the village, Shu runs into Noi who states his interest in finding Kluke and going to awaken her shadow. Meanwhile, Bouquet gets jealous when she hears from Marumaro that Shu went off to look for Kluke. The next day, Kluke leaves to tend to her students. At her house, Shu encounters Andropov who says that Kluke isn't here. Besides stating that he is looking for Kluke, Shu tells Andropov about what happened to Albarose and that General Logi's whereabouts are unknown. Meanwhile, Noi meets with Kluke. Andropov tells Shu that Kluke doesn't want to end up battling again. While the kids are napping, Kluke tells Noi on how she was treating the injured following a great battle and that one of the injured was Andropov. Also when brought up by Andropov to Shu, a flashback depicts Shu telling Kluke that Legolas is organizing a resistance against Rosekstan and states that she doesn't want any part in the resistance. After the flashback, a battle between Shu and Andropove then assume where Shu wins with little trouble due to Andropov's condition. Shu is unable to trample over Kluke and Andropov long found peace causing Shu to leave. Meanwhile, Noi secretly reawakens Kluke's Phoenix without her knowing and departs. Later that evening, Kluke returns home and meets up with Andropov.

Shu heads out to the wetlands at the edge of Logic. Meanwhile, Jiro is attacked by the sea shore by some soldiers in white and fends them off when a man named Vermillion shows up telling them to fall back as Jiro is not a shadow wielder. Moments later, Delphinium and Deathroy approach the soldiers' camp to look for Dr. Tarkovsky. After 2 days of waiting all spot a cloud that's not moving with the wind like other do. They were pursuing it till it landed on mountains, where the clash with Mikhail begins. Meanwhile, Jiro follows the caravan of the soldiers in white until Delphinium appears. Mikhail gains the advantage with his red dragon shadow against Shu. After a long fight, Shu fuses with Bouquet and Mikhail crumbles to dust. However, it appeared that the Mikhail was another Dragon Scale clone, when the real Mikhail appears.

Conrad and a Knight Master named Griz join up with resistance headed up by Legolas and Daner in a nearby city and joins him in exploring the ruins of the Investiture Beings there. Shu, Bouquet, Marumaro, and Noi arrive at the city as Lotarus is encountered by Delphinium and Deathroy. Deathroy unleashes Chimera as White Brigade's weapons fire at Lotarus. She manages to evade the weapons and Delphinium's shadow before turning into her dragon form. While Lota deals with Delphinium and Deathroy, she also unleashes winged creatures that attacks the White Guardians. Lota takes the opportunity to escape while Delphinium and the White Guardians are occupied. Shu meets up with Legolas and Conrad and they descend into the underground caverns that are underneath the city. Noi then reads the messages found on the floors of the cavern. When Shu has Blue Dragon punch the artifact on the wall, he is sucked in.

Noi reveals himself to be one of the 'Investiture Beings', but keeps it from Shu and the others to keep their trust. The battle with Shu and Mikhail rages on again with Mikhail unleashing his Red Dragon shadow even when Marumaro and Saber Tiger throw themselves in front of Mikhail's attack. Mikhail reveals his true form as the Red Dragon itself. Meanwhile, Lotarus notices the soldiers in white approaching. The warriors Vermillion and Furioso watch the fight recapping about Primella's prediction of Albarose' destruction when Dr. Tarkovsky appears identifying the Red Dragon as Mikhail as their tri-barrel technological weapons get positioned. Mikhail ends up overpowering Blue Dragon in fusion form. Shu refuses to give up when Mikhail starts attacking Noi for breaking the rules of the Investiture Beings. Then Noi transforms into his black dragon form, revealing himself in front of Shu and initiates the forbidden fusion with Blue Dragon to gain a new dragonite form and evening the odds with Mikhail. During the fight, the soldiers in white step in firing a tri-barrel weapon called the Brunack causing Mikhail to flee. The soldiers corner Shu and co. as Vermillion introduces them as the "White Brigade" and stated that their mission were absolute destructions of all shadows.