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 worries of Kluke being unconscious, while Jiro worries about defeating Nene. Shu and the others discovered that they still have a hold on the criteria on the suspect who killed the saineles. They say that the suspect is a age of 20 to 30,she has blue hair, and has perfume on her body. So, Shu and the others decide to get the extra seven pages to get stronger and defeat Nene.

Kluke has woken up and is good now. Shu and the others continue their journey to the book of origins. Now Shu and the others are in logic city in their journey.

Shu's informant Homeron is gathering information about the Extra Seven. Shu and Co. arrive at Flame Phoenix ruins. When Kluke disappears, she ends up in the area where she first encountered her Phoenix shadow and asks it how she can call upon its power again. Phoenix tells Kluke that the answers lie in herself. Kluke then receives a necklace and rejoins Shu and Co. When they find Jibral's scattered army being attacked, Shu and Co. join the battle. Upon defeating the robotic soldiers and their shadows, Shu and Co. are soon attacked by a giant robot. Kluke brings out her Phoenix Shadow to use its barrier to protect everyone enough for Shu to use Blue Dragon to destroy the giant robot. Meanwhile, Homeron receives news the mysterious woman who stole the Extra 7 is heading west.

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.

Conrad takes his soldiers to head to the west side to gather others that will fight Gran Kingdom. Homeron continues his infiltration to look for Castle Des La Teste's master computer. Gilliam and his followers Todd and Bishop attack the recently released prisoners resulting in Marumaro and Saber Tiger fighting Gilliam and Euphoria with Shu's Blue Dragon and Kluke's Phoenix joining the battle. Jiro and Zola fight Todd and Bishop. With the help of Phoenix, Marumaro and Saber Tiger managed to damage Euphoria. Andropov informs Gilliam to have his group retreat. As for Homeron, he learns the name of the white-haired woman to be Delphinium.

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.

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). 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.

Nene's flying fortress invades Raqueeva. When General Szabo questions Nene about General Logi's activity, Nene tells him to let General Logi handle Shu's group. On the trail of Logi's ship, Shu and Co. end up in battle with the Independent Flying Squadron again. This time, they've all been equipped with Power Boosters to make them more powerful and are instructed to fight them even if it is to the finish. Zola and Marumaro fight Gilliam, Todd, and Bishop while Cynthia and Schneider attack Shu and Co.

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.

After Gilliam, Todd, Bishop, and Cynthia's defeat, General Logi sends Andropov, Lemaire, and Schneider to take on Shu and Co. Zola faces off against Lemaire while Jiro and Marumaro fight Andropov and Schneider. Lemaire has Deucalion use its bazooka attack to create a crater where Lemaire will have the advantage. Shu faces off against General Logi. With Lemaire defeated by Zola, Kluke goes to help Shu while Bouquet infiltrates Logi's ship.

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.

Shu and Co. work on deciphering the Extra Seven pages that Bouquet shapeshifts into. Meanwhile, at Szabo's request, Nene orders General Logi to take a break from his mission. With the Extra Seven deciphered, Shu and Co. steal one of the Mechats from a Gran Kingdom airship and head to the ruins at Talta Village.

Arriving at the Blue Dragon's ruins, Shu and Blue Dragon have a confrontation with a shadow called Dark Dragon. After nearly falling for Dark Dragon's deceit, Shu and Blue Dragon engage it in battle matching attack with attack. Shu manages to overcome Dark Dragon.

Nene sends General Szabo to the capital of Galga to attack Shu and Co. Jiro is attacked by General Szabo. This time, General Szabo unleashes his Mighty Quartet to assist him. Minotaur manages to pull off a retreat to get Jiro out of there. After a brief talk with Kluke, Jiro is attacked by General Szabo and his Mighty Quartet. Shu and Kluke arrive as General Szabo merges with his Mighty Quartet to form Ultimate Szabo. As Shu unleashes Blue Dragon, General Szabo unleashes a giant robot to fight Blue Dragon. Zola, Marumaro, and Bouquet arrive just as Blue Dragon breaks the giant robot's left hand. Jiro and Minotaur knock Ultimate Szabo into the lake. After some attacks from Ultimate Szabo, Jiro and Minotaur create their own whirlpool and eventually destroy Ultimate Szabo as Shu and Blue Dragon destroy the giant robot. Delphinium tells General Logi that Blue Dragon and Minotaur have gotten stronger and part of the Extra Seven has been deciphered by Shu and Co.

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.

General Logi is informed on the development on the Extra Seven. Shu and Co. head to Marumaro's village. When Marumaro wants to fulfill the prophecy of the original Saber Tiger wielder, he has Saber Tiger remove the guardian statues from the top of the other Devees' houses causing the other Devees to get angry and chase them. Marumaro then goes on a beautiful girl-viewing activity causing one of them to issue a complaint to Marumaro's parents. Zola sends Shu, Jiro, Kluke, and Bouquet to stop Marumaro. After catching up, Zola tells them to lure Marumaro into the canyon. Marumaro and Saber Tiger managed to get through every trap and barrier to gain a new power. Meanwhile, General Logi heads off on his own and leaves Andropov and Schneider in charge of the ship.

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.

Kluke and Bouquet argue over which ruins to go to first, and Kluke derides Bouquet for being useless. Needing to refuel, the group enters enemy territory where they learn from an informant disguised as a soldier, Nene is on his way to the ruins of Bouquet's power.

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 group decides to take Nene down once and for all. Both sides unleash their shadows as Chimera counters their moves. After landing a hit on Chimera, Nene has it use Shadow Multiply for each shadow. Meanwhile, General Logi gets word that Zola and the others are engaging Nene and plans to wait for the outcome. Nene reveals that the captive children's strengths are flowing into him. After some history behind Zola and Nene are revealed, Nene has three of the Chimera clones charge up the Graviton Balls and has the other three keep the others at bay while Kluke and Bouquet get trapped before they can help Zola. Back on the ground, Legolas arrives with reinforcements to help Conrad against the Black Shadow units. Surviving Chimera's attack, Zola unleashes the true power of Killer Bat as it changes color and gets much faster. Shu and Jiro send Blue Dragon in to help her while Marumaro and Saber Tiger try to free Kluke and Bouquet. Zola manages to take down one of the Chimera clones, but is hit by Nene's attack.

Zola has been defeated while Marumaro and Saber Tiger free Kluke, Phoenix, Bouquet, and Hippopotamus. Shu and Jiro have Blue Dragon and Minotaur attack Nene. Nene combines the Chimera clones to form one large Chimera. Meanwhile, General Logi has dispatched his troops which will attack when Schneider and Andropov receive the command from General Logi. Nene uses Chimera's Dark Symphony attack which weakens his opponents. When Shu and Blue Dragon's attacks are countered by Chimera's attack, Shu falls unconscious. In a dream sequence, he encounters Lt. Dragnov and Homeron. Marumaro and Kluke are defeated as Jiro has Minotaur aim for the device on Chimera's forehead. Shu rises from his boulder grave for another bout with Nene. Assisting Jiro and Minotaur in attacking the crystal on Chimera's forehead, Shu and Blue Dragon learn that the crystal enabled Chimera to alter his elements. The limiter is unleashed as Nene and Deathroy merge with Chimera to form an amalgam of all three of them. With Jiro defeated, Shu uses every ounce of his power and manages to destroy Nene as Deathroy is shown lying on the ground. With news of Nene's defeat, General Logi gives the command and has Schneider take over Castle Des La Teste while Andropov attacks some Gran Kingdom airships. This is General Logi's act of his secession from Gran Kingdom which he announces.

Following the destruction of Nene, the children that Nene has captured have been returned to their families. With the struggle against Nene's forces finally over, everyone rejoices. Shu and Co. alongside the survivors of Jibral and their allied forces celebrate their victory after arriving at the city of Logic. At the local banquet, Shu, Kluke, Jiro, Marumaro, and Bouquet receive their medals. Meanwhile, General Logi is informed by Delphinium that following Nene's destruction, the remaining forces of Gran Kingdom are either fleeing or even deserting. General Logi tells her that they are leaving Gran Kingdom. After a very long speech, Legolas and Conrad inform Shu and the others that they have assembled soldiers to go after the remainder of the Gran Kingdom army. After travelling to a temple and finding out that General Logi had been there, Zola has Homeron the Original and his fellow Homerons look for General Logi. Later that night, Shu and Jiro discuss about what will be next now that Nene is destroyed. Meanwhile, Delphinium attacks General Logi for his act of secession from Gran Kingdom. Delphinium escapes and General Logi doesn't bother to let Andropov track her down. With Zola still away, Shu, Jiro, Kluke, Marumaro, and Bouquet wonder what to do next now that they've defeated Nene. As Conrad and Legolas lead thousands of men to hunt down the remainder of Gran Kingdom's forces, Zola finally returns and tells them that they will be heading to the Sealed Grounds. Meanwhile, Andropov and Schneider have increased the powers of their shadows Alubujem and Isabel for General Logi's next plot.

General Logi arrives in a ruined town owned by Gran Kingdom where General Orehill of Gran Kingdom's 3rd Squadron army is trying to set up a new world order. While traveling to the Sealed Grounds, Zola explains that the Sealed Grounds are a set of ruins relating to the Soldiers of Light as Andropov spies on them. Back at the ruined town, General Logi establishes it as the Rosekstan Kingdom which will be a Shadow Extremist nation. He also persuades General Orehill, the civilians, and the Gran Kingdom soldiers present to join his cause after showing them the Black Shadow Type Four (exo-suits that contain artificial shadows). Schneider informs General Logi about the information Andropov told him about Zola heading to the Sealed Grounds. General Logi and Schneider confronts the team on the path to the Sealed Grounds. General Logi faces off against Zola while Schneider and Andropov keep the others busy. General Logi recaps when Zola was with Gran Kingdom army before she betrayed them. The others unleash their shadows to fight back against Schneider and Andropov. Zola mentions to General Logi that she's after the truth of shadows. In order to learn about Zola's secret, General Logi instructs Andropov and Schneider to capture one of the Shadow Wielders. As Andropov charges toward Shu and Kluke, Blue Dragon uses his Blue Explosion attack to shatter Alubujem. However, Andropov has Alubujem use its remains to form a crystalline trap around Kluke. This enables Andropov, Schneider, and General Logi to get away. On the airship, General Logi states to Andropov and Schneider that he will get Kluke to tell her everything she knows about Zola and the shadows.