A boy named Shu is obsessed with knight masters learns that one has appeared in his village. Shu gets excited at this possibility and goes in search of him. His village gets attacked after finding the "knight master". Shu unleashes his true power after finding his friends are in trouble.

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.

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.

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 broke Valkyrie's shield (whose left wing ends up cut off in the process). The power surge of Blue Dragon's battle with Valkyrie results in a power surge that breaks the glass that's holding the pages. An invisible Bouquet seizes them, but runs into Delphinium who managed to detect her. Logi and Valkyrie managed to bring down Blue Dragon, but Shu gets enraged enough to bring Blue Dragon up to a powerful level. Andropov and Schneider managed to get Logi out of there at the last minute. A 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. However, Bouquet managed to memorize them enough for her to use Hippopotamus' shape-shifting to turn into copies of them for Shu and Co. to try and decipher.

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.

Two years after the world is freed from darkness, a young dragon escapes and crashes to earth. Shu and Bouquet have joined Legolas' Sarbin resistance against General Logi. Shu leads a supply raid on a Rosekstan airship, then rides with Bouquet to investigate the crater, and encounter a mysterious boy named Noi. All three find themselves prey to a Rosekstan fleet. But a red dragon appears and decimates the Rosekstan forces. While evading the red dragon, Noi uses his Tosen Kyuden ability on Shu. With Noi's help, the Blue Dragon returns. After a fierce battle, Shu and Blue Dragon cause the red dragon to retreat.

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.

Conrad, Griz, and Daner report what he has found underneath the city to Legolas. Upon remembering what Mikhail said, Noi tells Shu, Bouquet, and Marumaro that he is heading down into the ruins. Noi assumes his dragon form and flies down. While Bouquet and Marumaro have reached a disagreement, Conrad speaks to Shu about what to do with the Investiture Being ruins. Noi manages to get into the database when Lotarus in her dragon form arrives. A flying rock-like structure arrives floating above the city and is a threat if it lands on it. Shu unleashes Blue Dragon and checks it out. Panic occurs in the city as Griz and Daner speak with Bouquet and Marumaro. Blue Dragon attacks the rock structure as Bouquet, Marumaro, and Saber Tiger arrive to help. Bouquet and Hippopotamus merge with Blue Dragon and they attack the floating rock structure. Shu and Blue Dragon use whatever they can to destroy the rock structure and send its debris far. Lotarus takes her leave after this. Later that night, everyone is in the database room. As an eclipse occurs, secret data appears.