Marumaro and Bouquet unleash Saber Tiger and Hippopotamus to follow Blue Dragon into the artifact. Hippopotamus pulls a lever that causes Shu and the others to fall in as well. Noi finds ancient technology that opens a hole in the ground as he, Shu, Bouquet, Marumaro, Conrad, Griz, and Daner go down it. Upon coming to a room, Noi works on its keypads to learn about the technology. The security system is soon activated as thin robots attack. Noi manages to find a way out which they escape through. They soon come across a room where Mikhail in his Red Dragon form is recuperating. Mikhail wakes up and takes out Griz who tried to attack him. Shu unleashes Blue Dragon as Conrad does a failed attack on Mikhail. Marumaro and Bouquet unleash Saber Tiger and Hippopotamus to help Blue Dragon. Noi turns into his dragon form and merges with Blue Dragon while Bouquet and Hippopotamus merge with Marumaro and Saber Tiger. After taking a hit from the Blue Dragon/Noi combination, Mikhail escapes. Shu then thinks about what Mikhail and Lotarus have said.

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.

Shu, Bouquet, Marumaro, and Noi help two female bakers prepare a cake display for a town event to earn some money. But there are delays in the kitchen, and Noi and Bouquet has to stall the crowd until they are done. With help from Shu, they complete the cake display and use Saber Tiger to transport it there. When Blue Dragon bursts out the cake scaring the kids, Bouquet improvises by having Hippopotamus dress up as a superhero called Hipopotaman to fight Blue Dragon. Marumaro has Saber Tiger join the act to help Hipopotaman fight Blue Dragon. This only agitates Blue Dragon in the end who makes sure the party "ends with a bang".

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.

As the White Brigade prepares to attack Shu and the others, Shu fends off the White Guardians while Noi evacuates Bouquet and Marumaro away from the area. The White Guardians also retreats as Lotarus watches from afar. Mikhail is shown near a river badly wounded. Shu and Noi have a conversation regarding the events that occurred two years ago as the White Guardians continues their advancement. Later that evening, the village that Shu and Co. are resting turns out to be near the White Guardians' headquarters in the city of Nirvana. Bouquet uses her invisibility to listen out what the White Guardians is up to. Bouquet then unleashes Hippopotamus and takes the form of a White Guardian to throw them off track. Shu and Co. are spotted by some White Guardians, but are knocked out by Saber Tiger. Making their leave from the city, Shu finally encounters Primella in person.

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.

Mikhail leaves thereafter, before warning Shu that the fate of the world lies in the choices he and his friends make. Back with Logi's duel with the mysterious woman, she states that he was not qualified and in a flash sets Logi and Albarose ablaze. Watching from a distance were two tightly cloaked characters. Feeling the need to gather the previous partners being shadow users, Shu takes Bouquet and Noi to Marumaro's village to awaken Marumaro's shadow Saber Tiger. But starting out on a wrong foot sets Noi and Marumaro at each other's throats. To settle their differences Shu has Marumaro and Noi compete in different sporting events like arm wrestling, racing, and other events. When it comes to a card game, Noi wins and uses his Tousen Kyuden to awaken Saber Tiger. The Investiture Beings are in their meeting and have elected Shu as the World's Representative. Mikhail leaves to watch over Shu's progress.

Shu has a dream of a mysterious girl telling him to save the world. After Noi helps reawaken Bouquet's Hippopotamus, Shu and Bouquet talk about Noi including about his mysterious ability to revive lost shadows. Shu then tells Bouquet that something is not right in the world and says that they will be heading to Marumaro's village. Meanwhile, General Logi is in the middle of world conquest when his second-in-command Matilda tells him of an important matter. Rosekstan's capital Albarose is then invaded by a woman who has the same characteristic as Noi. Having his guards taken down, Logi faces the woman. The woman however wants a fair fight so she reawakens Odin from his slumber with her Tousen Genbaku. Shu's party later has a run-in with a mysterious man named Mikhail stating to be a 'Investiture Being', and also a shadow wielder whose shadow is a splitting red of the red dragon they fought before. Overwhelmed as their fight rages on, Noi reluctantly uses his Tousen Bardagir move that gives Bouquet and Hippopotamus the ability to merge with Shu, giving a new armored form for Blue Dragon to overpower Mikhail but not defeat him

In order to free the world of darkness, a sacrifice of the shadows must be made.

Conrad gathers soldiers to fight Gran Kingdom; Homeron continues to search for the master computer.

Shu must find confidence in his fighting.

Shu helps their waitress get away from two men who are harassing her.

When an evil kingdom attacks his village, Shu must awaken the legendary Blue Dragon.

Arriving in a local town, Shu recalls about his attempts to Jiro and Kluke to help him. This causes Marumaro to become concern and Bouquet to feel neglected. Marumaro ends up encountering dancing sisters Donna and Reina. When Marumaro brings them to Shu to cheer him up, the sisters end up dancing with Shu and Noi until Bouquet arrives getting into an argument with Shu. The sisters break from Noi and end up sucking the life out of Shu and Bouquet. Donna and Reina then perform while sucking the life out of some of the townspeople. Marumaro ends up deciding to correct this problem and obtaining Noi's help. Donna and Reina recall when they used to be down and out until Mikhail arrived and gave them Dragon Scales to make them more beautiful. This also caused them to absorb the energy of jealous people. When Donna and Reina leave, Marumaro and Noi emerge from their hiding spots as Noi tells Marumaro that Donna and Reina have the crests of the Dragon Scale on their necks. Marumaro and Noi end up disguising themselves as one person so that Marumaro can use his shadow power to deactivate the Dragon Scales starting with Reina. It doesn't go well when their disguise eventually fails. Marumaro ends up enticed by their beauty until Noi ends up not showing off his jealousy. Donna and Reina end up attempting to entice Noi with their beauty making Marumaro jealous. When Donna and Reina end up trying to absorb Marumaro's jealousy energy, Noi ends up biting Reina. Using Saber Tiger, Marumaro ends up driving the Dragon Scales out of Donna and Reina. Once the Dragon Scales were destroyed, those that they have drained energy from were restored. As Shu starts to regain his energy, he finds out that the name of the girl that has been appearing in his dreams is Primella. He ends up waking up alongside Bouquet. With Donna and Reina still unconscious with Noi stating that they won't remember a thing, Shu, Bouquet, Marumaro, and Noi take their leave. Shu finds out that Marumaro had been worried about him and Bouquet. Shu and Bouquet then end up in another argument revolving around what happened between him and Donna and Reina.

Homeron reveals that information regarding the Extra 7 is somewhere in Gran Kingdom's Castle.

Shu and the others want to hire an informant to help them find the Extra Seven.

Kluke is in a coma from the battle; Shu and Jiro encounter Legolas with updated information.

Shu and the others battle Nene; Kluke tries to awaken her shadow.

When an evil kingdom attacks his village, Shu must awaken the legendary Blue Dragon.

Marumaro finds himself in trouble when he flirts with an innkeeper's wife.

Zola and the team attack the fortress to free the captives; Shu manages to control the Blue Dragon.

Rosekstan begins their attack on Rudolph's war machine. Rudolph then unleashes his winged creatures, a bunch of Amethyst Dragons, a Moody Dragon, and a Phantom Dragon. Jiro, Kluke, Marumaro, Bouquet, Andropov, and General Logi unleash their shadows to attack the war machine while Noi looks for Shu. Meanwhile, Shu makes contact with Zola's spirit. As the battle progresses, Rudolph's war machine decimates most of the Rosekstan fleet. Just as one of the winged creatures is about to attack Jiro, he is saved by Delphinium and Deathroy (who have unleashed Chimera) as they arrive with reinforcements. Sleipnir fires its cannon at Rudolph's war machine but to no avail. Rudolph then fires the attack which decimates more Rosekstan airships as Noi charges towards the war machine.

Shu continues his fight with Rudolph. After taking a blow from Blue Dragon, Rudolph assumes his dragon form. Rudolph and the Shu/Blue Dragon are easily matched until Rudolph manages to strangle him. He repels Noi and the Bouquet/Saber Tiger. When Rudolph starts to finish off the Shu/Blue Dragon, Noi unleashes his power which enables his dragon form to get bigger. With this occurrence, Noi engages Rudolph. Both of them are easily matched. Right when Rudolph was about to finish off Noi, he is hit by an attack launched by the Shu/Blue Dragon. Rudolph enters a portal that he created and the Shu/Blue Dragon follows him into it. The Shu/Blue Dragon follows Rudolph into an area where he uses a war machine to defeat the Shu/Blue Dragon. The Investiture Beings' castle is starting to change shape into a large dragon-like war machine. Kluke uses her forcefield ability to protect them from its attack. Just then, Rosekstan's forces arrive as Shu's unconscious body is approached by Primella.

The battle between Rudolph and the Shu/Blue Dragon begins. Rudolph's shadow is matching blows with the Shu/Blue Dragon and nearly defeated Marumaro and the Bouquet/Saber Tiger. Rudolph starts to overwhelm the Shu/Blue Dragon. When Rudolph overwhelms the Shu/Blue Dragon sending him into a ditch with Primella and Dr. Tarkovsky falling after him. The attack also defeats Marumaro and the Bouquet/Hippopotamus. Noi even tries to have some words with Rudolph. Primella continues to glow and makes contact with Shu mentioning how she was a part of Zola before being separated from her by Killer Bat. After the talk, the Shu/Blue Dragon rises to continue his fight with Rudolph. Noi assumes his dragon form and tries to fight Rudolph, but to no avail. Before Rudolph can finish Noi off, the Shu/Blue Dragon saves him. Bouquet re-merges with Saber Tiger to assist Shu in the fight with Rudolph.

When Rudolph finds Lotarus guilty of what happened in her encounter with Noi, Lotarus is forced to fight Hildegard. When Lotarus manages to get Hildegard's elongated head, arms, and tail stuck, she is caught by surprise by the emergence of Hildegard's second head. When Hildegard frees himself/herself, Hildegard attacks Lotarus just as Shu arrives However, it was actually Bouquet in disguise as a diversion for Shu to have Blue Dragon attack Hildegard. Shu has Blue Dragon catch Lotarus and give her to Bouquet. Shu then engages Rudolph. After a brief talk, Shu and Rudolph unleash their shadows. Bouquet and Hippopotamus merge with Saber Tiger while Shu merges with Blue Dragon. As Primella starts to suddenly glow, the Shu/Blue Dragon charges toward Rudolph.

When Fagino attacks, Noi gives Shu the ability to merge with Blue Dragon to form a full version of Blue Dragon. However, something happens to cause Blue Dragon to not be able to move. Bouquet and Hippopotamus merge with Saber Tiger to defend him from Fagino. Shu manages to get control of it just as Marumaro and the Bouquet/Saber Tiger are defeated. Upon taking a beating from the Shu/Blue Dragon, Fagino assumes his dragon form and fights back. When Blue Dragon gets the upper hand, Fagino unleashes energies and quickly punches Blue Dragon. When Fagino and the Shu/Blue Dragon's attacks collide, Blue Dragon's attack goes through and destroys Fagino. News of Fagino's destruction reaches the other Investiture Beings. As Shu is recovering from the experience, Rudolph begins to broadcast a transmission throughout his realm where it revealed what happened with Lotarus' encounter with Noi back at the Investiture Beings ruins.

Rudolph recalls Hildegard and Fagino to his castle when the Mast Driver approaches their realm. As the Mast Driver approaches the area, strange aircraft attack. From within their ship, Shu and Marumaro send Blue Dragon and Saber Tiger out to fight them. With help from Noi, Blue Dragon and Saber Tiger trick the aircraft into crashing into each other. They finally arrive at the Investiture Beings' castle. Fagino is sent to attack them and unleashes his shadow. The other Investiture Beings watch from their castle.

Dr. Tarkovsky is given the status of the Mast Driver. Fagino's shadow does an attack on the Noi/Blue Dragon which causes Noi to separate. Marumaro and the Bouquet/Saber Tiger managed to destroy Blizzard Dragon. Conrad sacrifices his life to protect Shu from Fagino's attack. While Marumaro and Andropov keep Moody Dragon busy, Kluke has some words with Furioso. When Amethyst Dragon starts to attack them, it is destroyed by Rosekstan's Sleipnir airship as Jiro arrives. Hildegard has her shadow constrict Blue Dragon as Fagino moves in to eliminate Noi only to be intercepted by General Logi.

Following the vision of Primella, Dr. Tarkovsky leads Shu and the rest of the White Guardians to Z'Mey. At Z'Mey, Noi is researching the Mast Driver just as Bouquet, Marumaro, Kluke, and Andropov arrive. Shu also arrives with Primella as the conversation continues on Dr. Tarkovsky's airship. After the conversation, one of the soldiers enter and report that the Investiture Beings' winged creatures are heading their way. The White Guardians prepare their defenses against the winged creatures. As Conrad and Griz join the fight, the winged creatures overwhelm the White Guardians.

Shu gains an unlikely audience with Dr. Tarkovsky who learns about Vermillion's demise. The White Guardian soldiers set up a trap filled with food which Fagino falls for when he transforms into his dragon form. Some of the food he ate contained electrical spikes that seal up Fagino's mouth. As the White Guardian soldiers are assaulting Fagino, Primella receives another vision. Furioso does a fatal blow toward Fagino only to discover that it was a clone made from a Dragon Scale. Fagino emerges and overloads the spikes that were placed in his mouth. Fagino then attacks the White Guardian soldiers. As Fagino tries to destroy Furioso, Shu unleashes Blue Dragon and attacks Fagino. With Blue Dragon keeping Fagino busy, Furioso ends up slicing off his right arm causing Fagino to retreat. Dr. Tarkovsky then tells Furioso and his troops to spare Shu and Blue Dragon.

Having met up with Kluke, Bouquet and Marumaro work to prevent Primella's vision from coming true. Meanwhile, Noi researches the pyramid structure that just surfaced. Kluke finally learns about an attempt on her life as Lotarus arrives with some winged creatures. Shu and Primella meet up with General Szabo while General Logi's forces advance. Delphinium wakes up in a cottage and learns from the man who found her that Deathroy had kept her safe from Hildegard. Marumaro unleashes Saber Tiger to fight Lotarus while Bouquet gets Kluke to safety. Andropov arrives to help Marumaro. When Kluke and Bouquet end up in a flower field, Lotarus attacks Kluke. However, her attack missed Kluke and Lotarus departs with her attack force. Meanwhile, Shu, Primella, and General Szabo arrive at an area where the forces of Rosekstan and the White Guardians are going to fight each other.

Things aren't looking good for Rosekstan and Shu's allies. Just then, the Shu/Blue Dragon emerges with Primella in its hand. Primella wakes up as she is given to Dr. Tarkovsky and General Szabo. Rudolph emerges from the war machine and fights the Shu/Blue Dragon. They match blow to blow until Rudolph uses his intangibility to keep the Shu/Blue Dragon from hitting him and then multiplies to attack the Shu/Blue Dragon. With help from Primella, the Shu/Blue Dragon destroys the duplicates. The Shu/Blue Dragon collides its punch with Rudolph's punch. The hopes of Shu's allies, Marumaro's siblings, and even the thought-dead Conrad, Griz, and Daner help give the Shu/Blue Dragon the strength to fight Rudolph. Their combined attacks results in an explosion that destroys the winged creatures and the dragons that Rudolph had summoned. As the Shu/Blue Dragon falls to the ground, Rudolph starts to crack up and explode taking his war machine with him.

An assassin sets his sights on Jiro.

Shu and his friends encounter pint-sized Marumaro.

Shu and friends arrive at Jibral Castle; the group decides to solve the mystery of the ghosts.

Zola requests to view the "Book of the Beginning."

Pages from the "Book of the Beginning" are stolen with information about Shadow powers.

General Logi is waiting to ambush Zola's group as they approach Gran Kingdom.

Shu and Blue Dragon face General Logi.

Shu unknowingly strikes up a friendship with the enemy while traveling together.

Jiro must deal with memories of his tragic past; the group finds a strange machine in Nene's castle.

Shu and company arrive at Flame Phoenix ruins; Shu and company join forces with Jibral's army.

Cynthia is jealous of Bouquet's beauty; during a fight, everyone falls into Death Valley.

Homeron informs Shu of Delphinium, who is responsible for stealing the Extra 7.

Shu, Jiro, Marumaro, Homeron and the Norg crew are attacked.

Shu and the others head to Logi's battleship to retrieve the Extra 7.

Shu and Jiro struggle to take down Cynthia; Zola looks to launch her own attack against Logi.

Shu and the others go to Logi's ship to retrieve the Extra 7; Shu faces off against General Logi.

Kluke and Shu continue their battle with General Logi and Valkyrie.

Shu and Company start work on deciphering the Extra 7 that Bouquet shapeshifted into.

Shu and Blue Dragon confront Dark Dragon back at Talta Village; Shu manages to overcome Dark Dragon.

Nene sends General Szabo to the capital to attack Shu; Shu unleashes Blue Dragon.

Shu and Blue Dragon need to find a blacksmith for replacement parts.

Shu and Blue Dragon need to find a blacksmith for replacement parts.

Kluke solves chapter seven of the Extra 7 and uses the crystal on her necklace to power up Phoenix.

Bouquet and Hippopotamus try to solve the riddle of the fifth page.

Bouquet manages to shut down the Black Shadows; the gang decides they need to finish things off.

Both sides release their shadows as the group moves in to take Nene down; Legolas helps Conrad.

Zola has been defeated; Shu destroys Nene; Schneider takes over Castle Des La Teste.

Following the destruction of Nene, all the hostages are returned to their families.

General Logi establishes the ruined town as the Rosekstan Kingdom; General Logi faces Zola.

Shu and the others cope with Kluke's disappearance; Gen. Logi interrogates Kluke in his castle.