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

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 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 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.

In the episode Yusei Fudo dueled with Jack Atlas, where both players Summoned their aces, "Stardust Dragon" and "Red Daemon's Dragon" ("Red Dragon Archfiend"). Both monsters were upgraded to their "/Buster" mode ("/Assault Mode").