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 shows a mysterious battle in the past of Venice, Italy that Yusei knows did not happen in history before. 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. Afterward, Paradox flees to an earlier point in time. Jaden tells Yusei that he was pursuing Paradox, who stole his friends' cards. Yusei explains to Jaden the situation, and they decide to work together. Jaden pulls out a computer and uses the Manjome foundation's database to pull up an article, which states that Paradox killed Pegasus, using Stardust and other famous dragons.

Suddenly, Jaden's Neos card disappears like Stardust Dragon did, and this era starts to vanish as well. Yusei and Jaden travel back even further in time to try to prevent Pegasus's death. 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. Then, Yusei and Jaden arrive, and the Crimson Dragon transports them and Yugi 30 minutes back in time before Paradox's attack, in order to stop him, as Pegasus' premature death would drastically alter the course of history. After learning about Paradox's actions, Yugi decides to join them. Jaden notices his Neos is back and proclaims that right now, all their cards are safe from being destroyed by any alteration already done to time.

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 associated with Duel Monsters will be erased as well, and they challenge him to a duel. By combining the powers of their key monsters, Yugi, Jaden, and Yusei defeat Paradox, who is destroyed by the attack.

After the duel, Yusei, Jaden, and Yugi say that they will do what they can to make sure the future does not end up like Paradox's, and they say goodbye and the latter two return to their respective time periods. New Domino City returns to normal, and Yusei now feels that he can finally let go of the past and focus on the future.