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.