This episode introduces the basic aspects and rules of the Turbo Duel, Speed World and the new Synchro and Tuner monsters. Rally gives Yusei a stolen chip to upgrade his Duel Runner, but they are hunted down by Security forces. Yusei draws their pursuers away, and is dragged into a Turbo Duel against Trudge, one of the Security officers.

Yusei reflects on his past battle with Jack, vowing to win back his Stardust Dragon card which Jack took from him. Later, Tank, Nervin, and Blitz are challenged by a group of thugs, led by a person named Uryu. Yusei steps in to help his friends out, and ends up in a duel against Uryu with his Duel Runner at stake.

Yusei begins his ride to New Domino City to face Jack. On the way, Trudge forces him into another Turbo Duel. With only three minutes left to make it out of the pipeline, and Trudge's Gate Blocker preventing him from gaining Speed Counters, Yusei seems to be getting desperate - until he pulls out a special monster given to him by Rally.

Yusei, intending to win back his Stardust Dragon, meets up with Jack and challenges him to a Turbo Duel. The battle begins in the now deserted Duel Stadium. Yusei finds himself up against not only the fearsome Red Dragon Archfiend, but also his own Stardust Dragon which Jack placed in his deck.

Yusei and Jack's battle continues, with Yusei finally regaining control of Stardust Dragon. Both Yusei and Jack's arms burn as Stardust and Red Dragon Archfiend clash, and both their dragon-shaped birthmarks begin glowing. A third Dragon appears in the sky, blazing red. The duel ends with no victor and the appearance of New Domino City Security forces.

Yusei is arrested and sent to a detention center, where he meets an old man named Yanagi, who duels using what he calls his "Hidden Treasure" deck. Yanagi faces off against another prisoner, Bolt Tanner - and is shortly revealed to be a very poor duelist. Although lacking skills, he still cares deeply about his cards, something Yusei can relate to. Meanwhile, Goodwin reviews Jack's duel with Yusei, and discovers that, had they not been interrupted by the appearance of the Crimson Dragon, Jack would have been defeated.

Yusei has had enough of hearing Tanner making fun of Yanagi's cards and dueling skills, so he takes up Yanagi's deck and challenges Tanner to a duel, much to everyone's surprise, since Yusei is not dueling with his usual cards. Yusei wants to teach Tanner that every deck has a winning strategy, regardless of their value to others. Goodwin reveals to Jack the legend of the People of the Stars, the Signers and the Crimson Dragon.

Yusei is interrogated for information on his Dragon Mark, and Goodwin comes to the detention center to speak with him further. Yanagi tells Yusei what he knows about the Signers and the five dragons, and suspects that Yusei's Stardust Dragon may be one of the five. Meanwhile Jack duels Hunter again, but is off his game after his loss against Yusei.

Yusei is transferred to a different cell, away from Yanagi. His new cellmate, Alex, plans to escape and offers to take Yusei with him, but he refuses to leave without Yanagi and Tanner. Meanwhile, Armstrong has been harassing Tanner, and Yusei ends up in a duel against him, using a deck built with treasured cards given to him by all the other prisoners.

Yusei is caught in Armstrong's trap - not only is he forced to discard ten cards each turn, each Life Point lost also delivers a painful electric shock. Armstrong has disabled the electric current to his own Duel Disk, and thus does not feel any pain, until Alex breaks into the control room. He starts the current flowing again, but Armstrong just gets back up and keeps going. Despite the overwhelming odds, Yusei is able to pull through and win the duel. He is allowed to leave the prison.

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.

Yusei is able to escape from the police, but crashes his Duel Runner and is knocked unconscious. When he wakes up, he has been rescued and hidden from the police by twin duelists Leo and Luna, who live in the Tops area at New Domino City. Rejoiced to see that Yusei is alright, Leo asks him for a friendly duel-Yusei's Junk deck against Leo's Morphtronic deck. In the English version, Yusei suffers from amnesia following his crash, and Leo duels him in order to make him remember.

While preparing for the Fortune Cup with Blister, Yusei is reunited with Tanner and Yanagi. As they prepare to test out Yusei's Deck, they're confronted by Jack, who returns Stardust Dragon to Yusei. Later, Leo tells them about a duelist called the Black Rose Witch. (Known simply as the Black Rose in the English version). When she appears before them, the Mark of the Dragon on Yusei's arm begins to react.

The Fortune Cup has officially begun and the first duel pits Krieger against Leo, who is disguised as his sister Luna, as she did not wish to participate. Krieger's aircraft machine monsters are giving Leo's Morphtronic monsters a hard time. Meanwhile, Zigzix, Goodwin's scientist, puts his latest invention to the test: a device that detects signer activities. But Leo is unaffected while Luna is. Leo loses his duel and Zigzix finds out that Luna was in the stands during the duel.

The next duel in the Fortune Cup pits Gill de Randsborg vs. Akiza. Randsborg has learned from Goodwin and Lazar that Akiza is the Black Rose. At first, his Masked Knight leveled monsters seem to give him a clear advantage, until Akiza lets everyone in the stadium witness the dangers of her plant monsters, field spell card and finally, her Black Rose Dragon.

Next up in the Fortune Cup is a riding duel between Yusei and a mysterious caped duelist called Shira, but to Yusei's and Jack's surprise, the challenger is actually Hunter Pace who took the real Shira's place and disguise shortly before the duel starts. Yusei must now face Pace's deck filled with powerful Fire monsters, an improved deck which Pace planned to use against Jack later on.

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.

The first day of the Fortune Cup comes to a close. The audience attention is cast to an image of Krieger, who shall face Yusei tomorrow. As Tanner says that he wonders what kind of Duel Runner Krieger uses, something comes to Leo's mind, causing him to run off.

Krieger successfully summons Flying Fortress SKY FIRE and uses its effect to prevent Yusei to play his cards right. What Yusei doesn't know is that Krieger holds Goodwin responsible for the destruction of his home village.

The second round of the finals pits Akiza against Commander Koda. Koda has been ordered by Goodwin to expose Akiza as a signer, which didn't work on Akiza's last duel. Furthermore, Koda can expose his opponents' past to disable them. He doesn't take long to expose Akiza's troublesome reputation as the Black Rose, awakening painful memories to Akiza.

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.

Yusei wins his match against Akiza, but feels reluncant about it since he couldn't help her as much as he would have wished. He then rushes to Goodwin's tower in order to rescue his friends, but what he finds is Jack along Goodwin, and he explains how his rivalry with Yusei all began. Shortly after, the final duel between Jack and Yusei takes place, and to Yusei's surprise, his friends from Satellite are safe and sound, freed from the container that served as prison in Satellite, and they all watch Yusei as he duels.

The Fortune Cup Finals continue as Yusei summons Stardust Dragon to battle Jack’s Red Dragon Archfiend. As the battle goes on, the Crimson Dragon appears and Goodwin, revealing that he is the fifth signer and has a severed arm in a tank with the final Signer Mark shows Yusei, Jack, Akiza, and Luna bizarre visions of the People of the Stars and the future of New Domino City, being engulfed in a Spider shaped geoglyph of fire.

Greiger summons his Dark Synchro, which is Dark Flat Top, which allows him to special summon another Flying Fortress SKY FIRE, and then attacks Crow with it, which reduces Crow's life points to down 100. Crow crashes, but remains determined to win, and gets back into the game. Using a pot luck with his trap, he manages to defeat both monsters, but this in turn, allows Greiger to summon his Earthbound Immortal, Chacu Challhua. Crow manages to Synchro Summon Blackwing - Silverwind the Ascendant, and prepares to destroy Chacu Challua with its special ability, but then, he, Yusei, and Greiger notice that the souls used for its Chacu Challhua's summoning were the people of his village, and Greiger's siblings. Realizing it was the Dark Signer's fault, and not Goodwin's, Greiger wants to stop the duel, but the Earthbound Immortal refuses to give up, and takes over his body. As he struggles to regain control, Greiger asks Crow to finish the battle. Crow manages to defeat Chacu Challhua, freeing all the children, but the resulting impact causes the environment to collapse, and Greiger rams into him in order to save him from a falling piece of wreckage. Before he disappears, he asks Crow to look after his siblings and Yusei to beat the Dark Signers. With things settled, Yusei once again heads toward Kalin.

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. Back in the present, Kalin summons his Earthbound Immortal - Ccapac Apu, but Yusei manages to cancel out the attack and summons Stardust Dragon. Ccapac Apu attacks again, and the shockwaves almost send Kalin himself into the wall of purple flames, and Yusei reaches his hand for him. The power from all the Signers' marks transfer into Yusei, and he gains the Seal of the Crimson Dragon, which grants him a Tuner monster, Majestic Dragon, which appears in his deck, allowing him to summon Majestic Star Dragon and end the duel. Kalin finally forgives Yusei as he disappears into dust.

With Kalin and Ccapac Apu defeated, all the Satellite residents are returned. Just then, Roman uses one of his dark spiders to possess Trudge and talk to Yusei, coaxing him to find him at the Original Ener-D Reactor, challenging him to a duel. Lazar is seen talking to a mysterious figure. Goodwin goes to meet with Roman. Roman is shown with a shadow duel disk, and challenges Goodwin to a duel, as part of a promise they made. Yusei, Luna, Leo, and Trudge traverse down the crater, whilst Crow, who notices the army helicopters, takes a different route. Yusei encounters Roman on a bridge, who activates an explosion, causing a flux of Ener-D to appear underneath them. They start to duel and manages to attack Roman with Junk Warrior, although this in turn allows Roman to summon Earthbound Immortal Uru. Roman continues to put pressure on Yusei and manages to bring his life points down to 100.

After bringing Yusei's life points down to 50, Roman begins to tell him of what happened 17 years ago between him, Rex and Yusei's father. They were working on the Original Energy Reactor, but Professor Fudo wanted to stop the project when it started to look unstable. Roman had decided to travel to the Nazca lines, where he encountered a mysterious person, claiming to be from Yliaster, who knows about Roman's birthmark. The mysterious man convinces Roman to look into the light coming from the reactor, where he is struck by dark energy and is shown the history of the Earthbound Immortals and the mighty powerful Crimson Dragon. Meanwhile, Crow finds Rex, who explains that Professor Fudo was betrayed by Roman. He shows off four Dragon cards, but Professor Fudo manages to escape with three of them, but got severely injured in the process and entrusts the cards to Rex. Rex goes to confront Roman, who had severed his birthmark arm and given it to Rex Goodwin, telling him that he should unite the Signers and then come back to defeat him. He then overloads the Original Ener-D Reactor, after causing it rotate backwards, causing Zero Reverse to occur, and transforming Roman Goodwin into a Dark Signer, and results in the separation of Satellite from New Domino City. This kills Professor Fudo and Yusei's mother in the process, but not before he was able to get the infant Yusei to safety. Back in the present, Yusei manages to bring out Stardust Dragon, and after a series of counter traps from both sides, Yusei manages to defeat Roman. However, Roman warns him that if the signers don't seal all of the four control towers on time, then the King of the Netherworld would resurrect at sunset, and then he self-destructs himself the bridge, causing it to collapse, which results in Yusei to falling into the Ener-D pool.

With Roman's defeat, all the Satellite citizens, including Martha and Rally, are returned. Jack finally meets up with Carly, but she is reluctant to be helped and challenges Jack to a Turbo Duel. Initially, Jack is reluctant to fight and takes a lot of damage, but he starts to fight back, as he does not believe Carly is a person who would hurt people. Carly traps Jack in a vision where he is transformed into a Dark Signer by Carly and becomes destined to destroy the Crimson Dragon by her side. However, noticing Carly's glasses, Jack breaks free of this vision, and decides to fight for what Carly truly desires. Meanwhile, Yusei finds himself in a strange place surrounded by the spirits of those who died in the Zero Reverse incident. Due to Yusei's connection to the incident, they start to attack him, but he is rescued by a strong white light and the voice of a familiar figure.

Jack activates a Trap that lets Carly choose the outcome. He manages to break through to Carly and she makes the right choice. However, the Earthbound Immortal takes over her body, forcing her to continue the duel. Jack brings out his Red Dragon Archfiend in the hopes of freeing her. Meanwhile, the mysterious spirit reveals himself to be Yusei's father, who returns him to the real world. Carly summons out her Earthbound Immortal - Aslla Piscu, but Jack manages to stop its attack. Jack expresses his feeling for Carly, and then he takes the marks of the other Signers, gives him the Seal of the Crimson Dragon. Hearing the real Carly's pleas to end the duel, despite his objections, Jack synchro summons Majestic Red Dragon. Jack hopes to end the duel in a tie, taking him down with her, so that he can still be with her, but Carly activates a trap card so that only she would lose. Jack is able to do nothing but hold Carly tight, as she disappears into the Netherworld.

Akiza and Mina arrive at an abandoned amusement park where Ccarayhua's control unit is, shortly followed by Yusei's group, and a man claiming to be sent by Goodwin. Misty traps Akiza in a Hall of Mirrors, actually dueling her through the mirrors. She uses cards that block off drawing cards from the deck, and also shows Akiza the events involving Misty and her brother, Toby, who apparently met her at Arcadia Movement. Yusei is led to a room where Mina is found unconscious and is attacked by the man who turns out to be Sayer, who had survived his duel with Carly, and is determined to reclaim Akiza. He uses his psychic abilities to knock Yusei in a cage with Mina as it slowly fills with water. Trudge eventually finds them and tries to free them. Akiza is shown the moment where Toby was killed, which led Misty to become depressed and crash her car, transforming her into a Dark Signer. Akiza refuses to fight back and almost falls on a shard of glass, but is saved by Sayer, who whispers something in Akiza's ear that causes her to reawaken her dormant physic powers and summons Black Rose Dragon, which shatters all the mirrors, destroying the illusion, which reveals Misty's real location.

With Akiza's dormant physic abilities fully awakened, Misty activates her geoglyph. Trudge manages to free Yusei and Mina and Yusei goes to join Luna and Leo. Learning about Akiza's current state, Yusei goes to face Sayer, who reveals he is controlling her mind and was responsible for Toby's death. Misty summons out her Earthbound Immortal Ccarayhua. Sayer talks about the experiments he performed on Toby seeing that he did not have ultimate psychic powers sent him to an unknown location that not even he knows about. However, Yusei revealed he had activated an intercom on his duel disk, letting Misty know what Sayer had told him. Angered, Misty gets Ccarayhua to eat him, freeing Akiza from her trance. Misty apologizes to Akiza, but the Earthbound Immortal forces her to continue dueling. Akiza defeats her, setting her free, which results in her being sent to the netherworld. The New Domino City residents return, but a Dark Signer mark, the mark of the Condor appears in the sky.

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. Crow manages to destroy Sun Dragon Inti, whose special ability then causes Crow to take damage equal to Blackwing Elfin the Raven's attack points, and due to Sun Dragon Inti's temporary destruction, Moon Dragon Quilla then ressurects from Goodwin's graveyard. Then, Goodwin uses his Mark of the Dragon Head to steal all of the Signers' marks, and then he gains the Seal of the Crimson Dragon himself.

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 then sees a vision where he and the Goodwin brothers are inside the King of the Netherworld, and he sees all of the Dark Signers lying unconscious, floating in mid-air. The moment before the King of the Netherworld is destroyed, Rex Goodwin tells Yusei that he was successful in reaching him, and tells him to take care of the other Dark Signers, as they will be sent back to Earth. The Goodwin brothers decide to sacrifice themselves, so that the other Dark Signers can be revived. The King of the Netherworld explodes, the Altar of the Dragon Star (Rex Goodwin's dueling platform) is dissolved, and the Geoglyph duel tracks disappear, which causes Jack and Crow to fall. However, the Crimson Dragon catches both of them, and repairs all of the damage done by the King of the Netherworld. Peace returns, and the Daedalus Bridge is finally finished, uniting both Satellite and New Domino City.