While riding with Jack Atlas and Crow Hogan, Yusei Fudo finds his Stardust Dragon snatched away by Paradox—an enigmatic Turbo Duelist from a future era—who converts it into a Sin Monster mid-duel. Aided by the Crimson Dragon, Yusei pursues Paradox through a temporal rift and winds up in an earlier time. There, Paradox is locked in battle with Jaden Yuki, who still wields the might of Yubel and the Supreme King. Yet Paradox, having already seized Cyber End Dragon and Rainbow Dragon, has the upper hand and pushes Jaden to the brink. Yusei's timely arrival, backed by the Crimson Dragon, saves Jaden. The latter then explains Paradox's real goal: by plundering monsters from throughout history and corrupting them with darkness, he intends to slay Maximillion Pegasus, the very creator of Duel Monsters. If the game is never invented, the events of all three series would be erased from existence. Determined to stop him, Yusei and Jaden follow Paradox into the past, where they come across the King of Games, Yugi Mutou. But Paradox has already struck in this era, seemingly killing Pegasus and Yugi's grandpa while also snatching Blue-Eyes White Dragon and Red-Eyes Black Dragon. Once Yugi hears the full story, he resolves to fight side by side with Yusei and Jaden in the ultimate three-on-one duel, aiming to free the stolen monsters and save both the world and time itself before it's too late.