The player finds a "Speed Spell" card in their Duel Disk, causing everyone to believe that they are a Turbo Duelist. Since Yusei and Sector Security are the only Turbo Duelists in Satellite, they figure the player is from the City.
Since a Turbo Duelist is not complete without their Duel Runner, Blitz arranges for the player to buy a Duel Runner from Kuroe. After discovering it has no engine or CPU, Blitz goes to confront Kuroe, but ends up getting kidnapped. The player then ventures to the thugs' lair, where they duel and defeat multiple thugs in order to free Blitz.
After saving Blitz, Yusei gives the player a spare engine to use in their Duel Runner, before he leaves for New Domino City. A few days later, Rally gives the player a CPU. With the Duel Runner complete the player takes it for a test run.
A group of securities, led by Officer Trudge appear outside the group's lair, accusing Rally of stealing the CPU. Since they were using the signal from Rally's criminal mark to trace their location, Blitz used Yusei's jamming device to block the signal. The group split-up; Rally, Nervin, Blitz and Tank go one way and advise the player to ride their Duel Runner to the Old Highway. The player races out past the Securities, prompting Trudge to chase them. After the player outruns Trudge, they come back to the hideout. The player is planning to escape through the pipeline just like Yusei did earlier in the game.
After beating a test simulation, the player gets a chance to escape to New Domino. As the player enters the pipeline, Trudge immediately follows in pursuit. After outrunning him, the player gets caught by Security and is taken to the detention center having their Duel Runner and Deck confiscated.
In jail, the player reaches the Recreation room where Bolt Tanner is. Tanner has just won a Duel, with his opponent lying on the floor. Tanner taunts the defeated duelist by calling his cards trash, and the player then attempts to defend the defeated duelist by dueling Tanner with his Deck (like Yusei uses Yanagi's Deck in the anime). After beating Tanner, the player notices Yusei also getting escorted to his cell, and then receives a challenge from Mr. Armstrong. So the player has to collect cards from the inmates to create a Deck and use it to beat him.
After beating Armstrong, Armstrong calls off the deal and orders the Securities to seize the player. However, he is interrupted when Rex Goodwin appears on the scene, firing Armstrong and eventually releasing the player into New Domino City. Tanner passes the player his Ushi Oni card, telling them to seek a bar named Bootleg. Showing the card will allow for the player to come into contact with an acquaintance.
Upon arriving at the Bootleg, the player shows the bartender Tanner's card, but the bartender requests that the player complete some of his Duel Puzzles, as he's a Duelist. After completing 3 Puzzles, the bartender tells the player to wait outside - and upon exiting the bar, they encounter Blister, who escorts them to his hideout.
The player informs Blister of the plan to reclaim the Duel Runner and Deck. After some time of thinking, Blister gives the player a fake Security ID and Security uniform so that the player can sneak into the Security Impound Center and get their Deck and Duel Runner back. After sneaking past the guards and getting to the Duel Runner, the player is once again cornered by Trudge. The player then gets on the Duel Runner and promptly outruns Trudge once again through the Impound Center.
Upon escape, the player encounters Yusei, who also has reclaimed his Duel Runner and Deck. They both make a break to whatever cover they could find. As the player escapes Trudge they are guided by Leo to a place where they could hide out for the time being. Leo introduces himself and Luna, and then challenges the player to a duel. Upon winning, the player gets let in on a secret: there is an underground duel arena.
At the duel arena, the player and the twins witness Akiza beat yet another duelist. While people flee from the arena, the player feels a stinging pain as they notice a birthmark appear on their arm. Akiza notices this mark and promptly challenges the player to a Duel. After the duel, the birthmark disappears.
Several days later, the player gets informed of a Tag-Team Duel Tournament as they make their way towards the Duel Runner Shop. They also get into a Tag Duel with the twins, with Blister as their temporary partner. After the player finds a partner, they proceed to the Duel Stadium where they proceed through the tournament, facing Figaro and Corse (this opponent team may vary between who's chosen as the Tag partner), Blister and Tanner, and finally Leo and Luna. After winning, the player runs into Goodwin, who congratulates the player for their victory.
Some time later, the player runs into Tanner outside the bar and receives an invitation to the Fortune Cup. They shows this to Blister to know more about it, and is told to go to the Neo Domino Highway so as to sign up for the preliminary race. After passing the preliminary race, the player is confronted by Bass who then shows them how to play a Turbo Duel. After that, the player is also informed of the Speed Spells being sold at the shop.
The player then proceeds to the Duel Stadium where they face off against Trudge, Hunter Pace, and Greiger in the three Turbo Duels of the preliminaries. Following this, the player proceeds into the latter half of the Fortune Cup, facing off against Gill Randsborg and Akiza in two ground duels, and squaring off with Yusei in a Turbo Duel.
Upon finishing the duel, the player is about to prepare for the final duel with Jack Atlas, when they black out. They receive several flashbacks, and they wake up at a temple for the People of the Stars. They are then confronted by Rex Goodwin. It is revealed to the player that he was the one who grafted the birthmark onto the player's arm, as Goodwin plans to utilize the power of the Crimson Dragon. Goodwin then pits the player against 4 other clones - Alpha, Beta, Gamma and Delta - and the player has to defeat all 4 of them without replenishing life points in between duels (You'll just have to do the match over again).
Upon victory, the Crimson Dragon appears, but then shortly dissipates. Goodwin then realizes that he cannot simply do with replicas, despite the fact that intense duels will lead to the awakening of the Crimson Dragon. The player then blacks out again, and finds themselves back in their room, before the final duel with Jack Atlas. After defeating Jack, the player receives the Stardust Dragon card for Yusei. Goodwin aborts his plan to awaken the Dragon, and allows the player to do as they wish. The player then passes Yusei the Stardust Dragon card, and also receives a Travel Permit, allowing them to travel between Satellite and New Domino City.
Post storyline, Yusei has a new Deck with "/Assault Mode" support, the name of which references the game title, XLerator.