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.

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.

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.

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 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.

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.

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.

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.

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.

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.

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.

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 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.

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.

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.

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.

Hoping to save his friends from the clutches of Sector Security, Yusei Fudo challenges his old nemesis Officer Trudge to a Turbo Duel!

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.

Yusei uses Shooting Quasar Dragon to destroy all 5 of Z-ONE's current Temporal Machine Gods, and then manages to bring out Shooting Star Dragon to deal a lot of damage to Z-ONE, reducing his life points to 700. Z-ONE screams when he takes the damage, and then he crashes into New Domino City's central building. Yusei then removes all of his speed counters to draw Clustering Wishes, and sets it face-down. After Yusei and Z-ONE talk about the right of changing the future, Z-ONE angrily blasts a hole in the building, and flies back up into the sky. Z-ONE then feels angry at Yusei, for reducing his life points by such a great amount, and tells Yusei that he will now prove to him that hope, and the possibility to fix the future without New Domino City's destruction, which Yusei believes in, was nothing before his power.

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 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.

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.

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.