Although he is now out of the detention center, Yusei has noticed that he is being followed by Goodwin's agents. Luckily, he is taken by a former duelist named Blister, the man who Tanner told him could help get his Duel Runner and dueling deck back. After discovering Blister's past, Yusei infiltrates Goodwin's tower and finally recovers his Duel Runner and dueling deck, but not before Trudge shows up and challenges him to another Turbo Duel.

Yusei continues to avoid Trudge's brutal direct attacks as he attempts to escape with Bliser's help, but things only get harder from there. Despite the danger, Yusei resolves to restore Blister's faith in bonds with other people. When Trudge brings out Goyo Guardian, Yusei tunes four of his weak monsters together to summon Turbo Warrior.

The first round of the Fortune Cup is over, but Rex Goodwin is holding a consolation match, which opposes Professor Frank (Known simply as The Professor in the English version) versus the real Luna, much to Leo's disappointment. Not only Luna is reluctant to duel, but the duel itself is planned to uncover Luna's signer ability. Furthermore, Professor Frank has a stirring speech that sends Luna into a trance-like state, disrupting her dueling capabilities.

Luna engages in her duel with Professor Frank when she hears a mysterious voice saying: " You said...you'd protect the world of Duel Monsters spirits. " Then, the voice takes shape in the form of Ancient Fairy Dragon. Now, Luna must take all her courage and skill at hand to defeat Professor Frank's trump card.

Before the final rounds of the Fortune Cup commences, Yusei confronts and questions Akiza within a inner passage of the Dueling Stadium of why does she calls the Mark of the Dragon a "Wretched Mark." To which angrily responds that she hates and detests the person who carries a birthmark. Furthermore while becoming angry, Akiza feels that something remains hidden within her. Yusei, who is filled with various doubts, begins his Duel with Akiza.

The duel between Yusei and Akiza continues, and Akiza quickly gains the upper hand. Yusei, from his part, manages to put a good defense against Akiza's plant-type monsters, but also notices that Akiza takes a guiltiest pleasure at attacking him mercilessly.

After his victory over Jack in the Fortune Cup, Yusei is named the new Duel King. While Yanagi informs the gang about the Signers and the Dragon Birthmarks, Yusei is challenged by a mysterious man with a Spider shaped birthmark on his arm who is able to make the duel into a Shadow Duel. Yusei is surprised to find his opponent has a fearsome new type of monster, a Dark Synchro Monster. Meanwhile, a reporter named Carly tries to get the scoop on the new Duel King.

Following her release from security, Carly attends a premiere event and encounters a model named Misty, who predicts her death. When Angela, a rival reporter, reveals Jack was actually born in the Satellite, Carly decides to infiltrate the hospital to interview Jack. At that time, a Dark Signer spider possesses Trudge and challenges Jack, who is trying to leave the hospital, to a duel. Unable to use his fractured right arm, Jack decides to use Carly as his arm. They win the duel, but Jack is weakened and asks Carly to get him out of there without anyone noticing. Meanwhile, Goodwin shows Yusei the truth.

While preparing for his duel against Kalin, Yusei, Crow and Jack remember when they were all part of a duel gang, the Enforcers, who duelled rival gangs at night. The duel starts and Yusei takes a harsh attack due to the effects of the Shadow duel, which appears to be more dangerous in Turbo Duel.

Kalin summons his One-Hundred Eye Dragon, a Level -8 Dark Synchro monster, causing a real threat to Yusei. Yusei once again recalls his days in the Enforcers, and remembers how Kalin once saved his life. When he is almost burned in the fires of the dark barrier, Yusei also remembers when Kalin killed a member of Security and how the proceeding fight between them sparked Kalin’s hatred towards Yusei.

Akiza is taken to hospital where her parents, Hideo and Setsuka, meet up with Jack, Leo and Luna. Jack tells them that the only one who can save Akiza is Yusei, so Hideo travels to Satellite to talk with him. He tells him that when Akiza was young, he was unable to spend time with her due to work. When they finally were able to spend some free time together, a call from work interrupted, which frustrated Akiza and awoke her Signer powers and birthmark, hurting her father in the process.

Enduring the pain of Akiza’s attacks, Yusei summons Stardust Dragon to face against Black Rose Dragon and reach her heart. Still hurt by the loss of Sayer, Akiza unleashes her full power and constantly weakens Stardust Dragon. As Yusei gets hit by more attacks, Hideo steps in to protect him and try and reach Akiza, taking some damage in the process.

While flying to the Satellite Akiza asks about Yusei’s father and Mina explains to everyone what his father did. She also explains what happened 17 years ago and that Yusei is city born. Yusei, Jack, Akiza, Leo, Luna, Mina and Trudge arrive Martha’s house where she and Blister are waiting. Martha informs everyone that Crow, Rally and the others have gone missing, and offers everyone a meal. Then Yusei answer Martha’s question if the girl that’s sitting there at the table is Akiza and then Martha states he saved her.

As Roman prepares for his Earthbound Immortal summoning, Yusei tries his best to postpone it and Martha and Trudge hurry to save the children. However, Roman then speeds up the process and is able to summon his Earthbound Immortal, Uru. Thankfully, Jack arrives on time and forms a barrier around the children to stop their souls being sacrificed. Roman then reveals that not only was he an assistant to Yusei’s father, but is also Goodwin’s brother and the one responsible for the Zero Reverse incident. Yusei manages to deflect an attack from Uru’s attack, but it hits a building Taka, Martha and Trudge were hiding in.

Yusei finally catches up with Kalin and start what Kalin calls 'The Last Duel of the Enforcers'. Yusei hopes that this duel will rekindle their friendship. After the Enforcers took over the Satellite, Kalin kept looking for enemies. When those enemies started including young kids, Crow and Jack left the team, leaving just Kalin and Yusei. When Security shows up in Satellite with Duel Runners and Kalin plans on destroying them, Yusei also quits the team. Kalin decides to attack Security, getting their attention by blowing up some confiscated Duel Disks. When Yusei, Jack and Crow catch wind of Kalin's actions, they go to look for him and find him cornered in a building ready to stand off against Security. Back in the present, Kalin summons his One-Hundred Eye Dragon and begins to utilize his Handless combo.

Yusei defeats One-Hundred Eye Dragon, but is fully aware that it allows Kalin to draw his Earthbound Immortal to his hand. Back in the last days of the Enforcers, in a flash-back of Yusei's memories, Yusei, Jack and Crow try to talk sense into Kalin, and they all end up running away from Sector Security. One Sector Security officer pins down Kalin, but he manages to jump on his Duel Runner, causing him to crash with a bad head injury. He tries to finish him off but Yusei stops him. Yusei tries to pose as the leader of the Enforcers in order to protect Kalin, but the chief of Sector Security at that time had already figured it out that Kalin was the real leader of the enforcers, and Kalin becomes furious when he sees his hand on Yusei's shoulder, thinking Yusei had ratted him out. Kalin then gets harsh treatment in prison, losing his deck, and he was eventually convinced by the voice of Roman to become a Dark Signer.

As the Condor geoglyph shines in the sky, a massive monster emerges from the Original Ener-D Reactor and heads towards the Condor geoglyph over New Domino City, which was the King of the Netherworld. The Crimson Dragon appears and sends everyone to the front of a temple (the Altar of the Dragon Star), where they find Goodwin, who reveals himself to be a Dark Signer. Then, he transfers Roman's mark of the Dragon Head from a canister to his left arm, destroying the metallic arm that was covering it at the same time. He challenges Yusei, Jack and Crow to a Turbo Duel in the air. Goodwin reveals that he lost the duel with Roman prior to his battle with Yusei on purpose, and became a Dark Signer in order to end the pointless cycle. He summons out both a Synchro monster; Sun Dragon Inti, and its Dark Synchro counterpart; Moon Dragon Quilla. He also reveals he was the Legendary turbo duelist who constructed and flew across the Daedalus Bridge.

After being dealt some direct damage due to the cooperative efforts of Yusei, Jack and Crow, Goodwin is able to summon his Earthbound Immortal - Wiraqocha Rasca, absorbing the souls of New Domino City. Then, the King of the Netherworld spouts forth several beasts that attempt to attack the players. However, they are saved by Black Rose Dragon and Ancient Fairy Dragon. Crow sacrifices himself by playing a trap card in order to protect Yusei from Wiraqocha Rasca's special ability, and falls unconscious. Goodwin coaxes Jack into attacking him, but after he gives in and loses some life points, Goodwin's statement of becoming a dark signer causes Jack to remember what Carly taught him and decides not to do things his old fashioned way anymore. Goodwin laughs at the idea of the bonds of true friendship and love, saying that destiny is all that there is.

Goodwin reduces Jack's life points to 1, and gets the King of the Netherworld to attack him, causing him to crash. Yusei's life points get reduced to 1 too, before he summons his Stardust Dragon and takes advantage of the traps Crow and Jack placed beforehand. As Yusei tries to reach Goodwin, which he successfully does, he regains the Signers' marks from him. Furthermore, Yusei gains Roman's mark of the Dragon Head, and the mark of the Tail that Yusei used to have transfers over to Crow. Yusei then takes the marks of the other 4 Signers, and gains the Seal of the Crimson Dragon. Then, he summons the Majestic Star Dragon and destroys Earthbound Immortal Wiraqocha Rasca, which defeats Goodwin. Then, the Crimson Dragon envelops the Majestic Star Dragon, infusing it with the power of the Crimson Dragon, and dives into the King of the Netherworld.

Yusei wakes up to find himself being carried away inside a truck after being ambushed by someone named Ichiro wanting to recruit him for the Grand Prix. When Jack, Crow, Akiza and Mina hear about his capture, they go to look for him. Akiza manages to locate the truck Yusei is captured in, and is surprised to find no one is driving it. Akiza uses her powers to break it open, but ends up trapped on their with Yusei when the truck speeds up. They escape, but are then challenged to a Turbo Duel by a mysterious rider. She brings out a fusion monster whilst Yusei responds with Junk Warrior, and Akiza finds herself moved from witnessing a Turbo Duel first hand. The rider then brings out her ace monster and reveals herself to be a woman named Sherry Le Blanc, hoping to recruit Yusei to her team.

The duel between Yusei and Sherry continues, with Akiza insisting that she stay and spectate. Yusei brings out Turbo Warrior and deals some damage, and eventually destroys her monster. However, it leaves him in a point where Sherry can win if she draws a Speed Spell, using Speed World 2's effects. Sherry then tells Yusei that she's entering the WRGP to avenge her parents who were killed by Yliaster. Just as Yusei is about to summon Stardust Dragon, Ichiro appears and tries to drop a truck on them. Akiza uses her powers to materialize Stardust Dragon and stop the truck, and Sherry's guardian, Elsworth, beats up Ichiro and his gang. Due to damage to the Duel Lanes, the duel is called off, but they promise to duel again. Akiza is left with a newfound respect for Turbo Duels.

Yusei arrives in a desert town called Crash Town, after receiving a letter from a woman named Barbara that Kalin was in trouble. She explains that in this town, there are battles at sunset between the Malcolm family and the Radley group. Yusei is surprised to find Kalin siding with Radley's group, and notices a change in his personality. Kalin uses his Handless Combo and quickly defeats Malcolm's challenger, who is taken away to become a slave in the mountains. Yusei tries to reach Kalin, but he doesn't answer him. Barbara tells Yusei the only way to save him is to beat him in a duel to separate him from the Radley family. Yusei decides to join up with the Malcolm family, earning his place by defeating three of Malcolm's men in one turn, with his Nitro Warrior.

Kalin still has memories of when he was a Dark Signer, and doesn't even find encouragement from the words of a young boy. Barbara mentions a plan involving using dynamite to aid Kalin's escape following their duel. During the next sunset, Yusei duels Kalin, who quickly puts his Handless Combo into effect. Kalin laments that he was never able to forgive himself for the actions he took as a Dark Signer, and has been looking to die, saying he'll be satisfied if Yusei defeats him. Yusei manages to take the lead, but Kalin still has tricks up his sleeve.

Kalin summons Infernity Doom Dragon, while Yusei summons Stardust Dragon. Using an equip monster, Yusei manages to defeat Kalin. However, Barbara betrays Yusei, attacking him whilst Kalin is taken away. The Malcolm family's top dog, Lawton, then appears and duels Radley, beating him before he even gets a turn. Barbara and the Malcolm family had used Yusei all along to remove Kalin from the Radley group so they would be easy prey. Yusei, along with Kalin and Radley, are taken to the mines and given shock collars. Yusei finds a means of escaping, but Kalin still refuses to be helped. Meanwhile, Nico and West sneak off with Yusei's Duel Runner.

Yusei knocks out Kalin, so they can escape, stumbling upon a graveyard of lost duelists. They then encounter Nico and West who have Yusei's Duel Runner, and learn that their father is still inside the mines. Lawton then finds them, so while Kalin and the kids look for their father, Yusei distracts him with a Turbo Duel. Lawton immediately summons Gatling Ogre, but Yusei's manages to delay its One Turn Kill ability. However, Lawton soon replaces it with Full Armor Ogre. Meanwhile, Kalin and the kids escape on a mine cart and arrive in a different mine. They become surrounded, but Kalin fights them off as West and Nico find their father, setting off to escape again. Yusei manages to beat Full Armor Ogre, but Lawton manages to resummon Gatling Ogre, putting Yusei in a position where one card could mean his defeat.

As Kalin escapes with the kids and their father, Sergio, the pursuers start activating the father's shock collar, but Kalin manages to stop it though nearly falls off the kart in the process. Yusei manages to avoid losing to effects, but Lawton instead summons a more powerful monster. Kalin's group are directed towards a deadly gap, so West and Nico's father jumps to change the tracks to safety, and Sergio falls into the abyss in the process (and dies). Yusei manages to summon Drill Warrior from his graveyard, and Kalin knocks into Lawton before he can respond to it. Lawton then throws some dynamite which sends everyone flying, with Yusei and Kalin falling into a canyon. Lawton kidnaps Nico and West, and along with Barbara overthrows Malcolm. As Yusei and Kalin visit the father's (Sergio) grave, his duel disk reacts to Kalin, who decides to fight with Yusei.

Barbara starts forcing members of the Malcolm family to duel each other to provide new workers for the mines. Yusei and Kalin arrive and challenge Lawton to a duel for Nico and West's freedom and to liberate the town. Lawton gets a handicap to start with 10 cards, giving him easy access to Gatling Ogre's ability. Kalin stops Yusei from negating Galting Ogre's effect and gets attacked. However, he has a special monster, Infernity Zero, whose ability allows him to remain in the duel even with 0 life points, though he will lose if he gains 3 Doom Counters. Lawton manages to destroy the card Yusei used to negate Gatling Ogre's effect in their last duel, but both he and Kalin manage to defend against Lawton's attacks, and Kalin manages to bring up his defense.

Yusei summons his Nitro Warrior and beats Gatling Ogre, dealing some damage to Lawton. However, Lawton summons out Long Barrel Ogre, and Kalin gains another Doom Counter, but Yusei sacrifices his Nitro Warrior to keep Kalin in the game. Kalin and Yusei both summon out their Infernity Doom Dragon ,and Stardust Dragon, but their attacks don't get through. Barbara threatens to harm Nico and West if Yusei and Kalin don't surrender, but the Malcolm family stand up against her. Lawton tries shooting his Shock Gun at Kalin, but is stopped by the arrival of Crow and Jack, who had brought along Sector Security to free all of the miners. Lawton sets off some explosions to escape, but Kalin catches up to him to finish the duel. Lawton makes an assumption about Kalin's cards, but he is defeated, thanks to the effects of Kalin's monsters. Lawton and Barbara are arrested by Sector Security, Crash Town is rebuilt as Satisfaction Town, and Kalin stays behind to look after Nico and West.

Greiger has a vision of Jack being destroyed by his own power, so calls both him and Yusei over to the Nazca plains. He talks about how he had built a temple to help seal off the Earthbound Immortals, but lately has been troubled by the appearance of what's known as the Crimson Devil. Greiger warns Jack that using his general power tactics will destroy him, but Jack insists he can only fight using power. Greiger suggests a turbo duel, but Jack is surprised to find his opponent is his little brother, Max, who appears to be possessed by something. Jack summons out Red Dragon Archfiend but finds himself having trouble against Max's special deck. When Jack attacks, he finds himself attacked by his own power just like Greiger's dream, and the duel is called off. Jack becomes defiant about abandoning his power tactic and drives off.

Jack arrives at an abandoned village where he encounters a strange Familiar who reveals himself to be the Crimson Devil's servant, who offers him a chance to gain great power. Meanwhile, Greiger comes to a conclusion that the actions of him and Max were those of the Crimson Devil. Jack, seemingly in a trance, goes into a temple that Greiger had built, leading him to where the Familiar challenges him to a duel. Yusei and company try to follow but are stopped from interfering by the Familiar, who reveals that if Jack loses, his body will become a host to the Crimson Devil, and cuts them off from Jack by creating a very narrow platform, and seals off the only exit. The Familiar announces that he, Greiger, and Max will all become sacrifices to the Crimson Devil. Jack struggles against the Familiar's Yomi deck, which punishes power play.

Jack summons out Red Dragon Archfiend, but is still hampered by the Familiar's Yomi deck, though eventually manages to deal some damage. The familiar tries to use the Crimson Devil's power to knock Jack off his platform, but he hangs in there. Greiger is reminded of a legendary Signer called Burning Soul who once defeated Scar Red Nova alongside the Crimson Dragon, believing Jack to be his descendant. Jack starts to play more strategically and deals more damage to the Familiar. The Familiar becomes angry and summons a powerful monster, bringing the release of Scar Red Nova closer. Just then, Jack produces a Burning Soul and, with the help of the Crimson Dragon, also known as Quetzalcoatl, seals the Crimson Devil forever into the card of Scar-Red Nova Dragon, and performs a 'Double Tuning' to summon that monster and defeat the Familiar, who was later killed by a collapsing wall during the destruction of the temple, due to the power of Scar-Red Nova Dragon's "Burning Soul" attack.

Ragnarok's 2nd turbo duelist, Broder, takes over and uses Thor's special abilities to knock Jack out. Crow enters the fight, but his attacks prove ineffective against Broder's traps, and he takes a lot of damage from Thor's attacks. Noticing the support Crow gets from the children, Broder explains how he came across a similar group of children, expressing his desire to fight Yliaster in order to protect them. Crow brings out Black-Winged Dragon, but Broder brings out his Aesir, Loki, which destroys Crow's Black-Winged Dragon.

With just 50 life points left, Crow's supporters almost get into danger while trying to cheer him on, reinvigorating Crow's resolve, and he soon manages to revive Black-Winged Dragon. Then, Crow activates a trap card from the Graveyard, which clashes with Broder's trap, knocking them both out. Yusei begins his round against Halldor, who quickly summons his Aesir, Odin.

Yusei begins his battle against Jakob, using Crow's trap to bring out Stardust Dragon when Black-Winged Dragon gets destroyed. Jakob then activates a trap, which brings out Grannel Attack 3, while reducing Yusei's life points to 2,800. Jakob shows Yusei and the others a twisted future where New Domino City is completely destroyed. Due to Synchro Monsters and Ener-D evolving the world at an incredible rate, a war broke out and the Ener-D reactor eventually exploded, destroying most of the world. The Yliaster trio also unveil their memmories of despair. In the future, they see everybody Synchro Summoning, and as a result of them using Synchro Monsters to achieve their own greedy desires, the Machine Emperors show up one day, and begin killing humans. In the vision, as Lester was running with his parents to safety, a Grannel shot his parents down. Lester in the vision, then wails at the death of his parents, the ones who loved him.

Jack, Leo and Luna reach the second gear, where they are shocked to see that Aporia has survived the crash, and that he is waiting for them. He forcefully attaches devices onto them, which pierce into their hearts whenever they take damage from the duel, meaning that they will die if their life drops to zero, with the only way of removing them is to defeat him in a three-on-one duel. Aporia activates the field spell Fortissimo the Mobile Fortress, and combines with it. Aporia also sets a trap which blasts players with real damage whenever they summon monsters. Although Leo promises to protect Luna and help Jack, Aporia counters each of his traps, making things worse for his allies. Furthermore, Aporia's attacks leave both Jack and Luna in critical states, and leaves Leo in despair.

As Jack, Leo and Luna struggle to survive, Aporia summons his key monster, Machine Divine Emperor Dragon Asterisk which will inflict 1000 points of damage to anyone who tries to Synchro Summon. Lamenting that he hasn't been able to protect anyone, Leo risks some of his own life points to protect Jack and Luna and weaken Asterisk. Leo then summons Power Tool Dragon and Ancient Fairy Dragon and gets hit by the 4,800 points of effect damage, bringing his life down to zero, causing him to die. The shock of Leo's death puts Luna in a critical state, as her life points gradually starts to drop, as her pulse weakens. However, Leo comes back to life with 100 life points, thanks to Ancient Fairy Dragon, and his Morphtronic Lighton's effect, and becomes the sixth and final Signer, with the Mark of the Crimson Dragon's Heart.

Leo uses Life Stream Dragon to counter Asterisk's, and Fortissimo's damage effects, and to restore everyone's life points to 2,000 (not including Aporia), which puts Luna out of the danger of dying. Seeing that his efforts to inflict damage to the Signers has failed, Aporia gets really agitated. Aporia then activates a trap to prevent Synchro Monsters from attacking, but Luna uses Ancient Fairy Dragon's ability to destroy his field spell, and activate one of her own that supports Synchro Monsters, allowing Jack to bring out Scar-Red Nova Dragon. The destruction of Fortissimo causes the fortress' structure to shake violently, and begin to collapse. Aporia manages to bring out Machine Divine Emperor Mechanicle Infinity Cubic to increase Asterisk's attack points, but Leo and Luna use their traps and dragons' abilities to weaken it. Jack then destroys Asterisk by attacking with Scar-Red Nova Dragon, which defeats Aporia, who falls to his "doom" with a feeling of hope in his heart.

A few years have passed since Z-ONE's defeat. The Public Safety Maintenance Bureau has dissolved into a city hall, with Lazar becoming the city's mayor. Yusei has become a scientist who supervises the completion of a new Ener-D mainframe, titled Fortune, to ensure the safety of the city. Crow had become a highway patroller getting an invitation to an overseas leagues, Akiza plans to study abroad to become a doctor, and Leo and Luna receive a mail from their parents asking them to leave New Domino City to live with them, leading everyone to wonder about the future of Team 5D's. Jack arrives after training with (defeating) several other duelists, wanting to leave New Domino City for a World League, in order to fulfill his dreams of becoming the World Duelist King, and Yusei challenges him to a duel, to decided the Signers' futures.

Yusei summons Nitro Warrior, but Jack manages to counter its attack and summon out Exploder Wing Dragon to destroy it, though Yusei manages to beat it with his Turbo Warrior. As the others watch the duel, they recall how Yusei had managed to change their lives. Jack then brings out Crimson Blader, which destroys Turbo Warrior and prevents Yusei from summoning more monsters during his next turn, but Yusei manages to survive Jack's attacks before Stardust Dragon and Red Dragon Archfiend return. Jack then summons out Red Nova Dragon, with a power of 6,000 attack points.