As Yusei Fudo ponders the state of New Domino City, Jack Atlas and Crow Hogan cheer him up with the idea of riding on their Duel Runners. As they ride, a mysterious Turbo Duelist called Paradox challenges Yusei to a duel. Yusei summons his Stardust Dragon but Paradox seals it inside a card and disappears with it. They later discover an article that says Paradox killed Pegasus with Stardust and other famous dragons. Compounding the situation, New Domino City is vanishing. As a result, the Crimson Dragon appears, giving Yusei’s Duel Runner the ability to travel through time.
In the past, sometime after the GX era, Jaden Yuki is attacked by evil versions of stolen monster cards in Venice, Italy, including Stardust Dragon. As Paradox prepares to kill Jaden, Yusei and the Crimson Dragon arrive and protect him. Jaden was pursuing Paradox, who stole his friends’ cards. Years earlier, Maximillion Pegasus is holding a duel in Domino City, which Yugi Muto is attending with his grandfather. Paradox uses his newly acquired monsters to attack the event, killing Pegasus, Yugi’s grandfather and several bystanders, but Yugi survives. Yusei and Jaden arrive and take Yugi with them 30 minutes back in time before Paradox’s attack in order to stop him, as Pegasus’ premature death would bring the existence of Duel Monsters to an end, radically changing the course of history.
The trio then confronts Paradox, who reveals that he comes from a future beyond Yusei’s in which the world lies in ruins, and claims that the only way to fix it is to eliminate Duel Monsters from history. However, the three heroes protest that by doing so all the future events and people will be erased as well, and challenge him to a duel. By combining the powers of their key monsters, Yugi, Jaden and Yusei defeat Paradox, who disappears. After the duel, Yusei, Jaden and Yugi say goodbye and the latter two return to their respective time periods. New Domino City returns to normal, and Yusei vows he will fight to protect the future so that he can meet Jaden and Yugi again some day.