The trio return to their garage where Leo and Luna come and show everyone an article they found on Wikipedia about Pegasus and Yugi. Jack says Yugi was the greatest duelist that ever lived. The article says that he died a virgin and his last words were "Oh god I've wasted my life." The article also says that dragons showed up and destroyed most of Eastern Europe ten years ago. In the picture of the dragons is Paradox, and the article notes that he stole Yusei's card to use it to destroy the past. Then the world starts disintegrating, but Jack thinks it's snow. Using the power of the Crimson Dragon, Yusei travels to Jaden's time, where Jaden is still trying to explain to Paradox that his name isn't protagonist. Jaden gets hit by Stardust Dragon's attack, and his card Neos is stolen. Stardust attacks again but Jaden is saved by the Crimson Dragon. Paradox leaves Jaden's time for some reason.
Yusei and Jaden introduce themselves. Yusei hates Jaden for being happy all the time. Yusei reveals that he is from the future but he can't give away any spoilers, since doing so would cast them into a world where time and space have no meaning. Yubel and Professor Banner appear next to Jaden, and Jaden tells Yusei he can see dead people. Jaden opens the internet and finds they need to head to Yugi's time, where Pegasus is going to release his new trading cards at the "gayest event ever". At the event, fireworks go off and Yugi's grandfather thinks that America is invading again. Paradox uses his three dragons to destroy several buildings, killing Pegasus, Grandpa and hundreds of innocent citizens. Yugi breaks down crying, but then he revealed he just wanted an oscar award. Yugi gets picked up by Yusei and Jaden. Yusei and Jaden introduce themselves, but refuse to give Yugi spoilers on whether or not he dies a virgin. However, Yusei tells Yugi that he will beat Jaden at the end of GX, because "It's not a spoiler if it's obvious". They assess the situation with Yugi, who realizes Grandpa is really dead and hasn't been sent to the Shadow Realm, a concept that confuses Jaden and Yusei since it didn't appear in GX or 5D's. The trio travel back in time to before Paradox launched his attack, and decide they need to create a diversion to evacuate the area, so Jaden shoots at the stage with a blast of energy. Paradox appears and takes off his mask, which seemed pointless to be wearing in the first place since none of the three protagonists know who he is. Yami whispers something to Yugi and they initiate the "Super Special Awesome Sexy Transformation Sequence... in 3D!". Paradox decides on the turn order which Yugi thinks is unfair.
Paradox activates Malefic World to intimidate the protagonists, which fails as they think it's a nice change of scenery. Paradox explains that he believes that card games destroyed his time and he invented time travel so he could travel back in time to murder Pegasus, but cannot come up with a sensible explanation for his other murders or card thefts. He is also unable to explain exactly how card games destroyed the world, simply saying that he was told someone played a card game and the world ended on the spot. Yugi tells Yusei that the duel will take place with feet firmly on the ground, not on motorcycles, which Yusei clearly understands. Throughout the duel Yusei and Yami have several romantic moments, but each time Yusei hears the song "Careless Whisper", reminding him that if he has an affair with Yami then his girlfriend (the motorcycle) will break up with him. Yusei Synchro Summons Junk Gardna, which Yugi uses to screw around. Paradox summons Malific Cyber End Dragon and Malefic Rainbow Dragon, the latter of which angers Jaden since it's his best friend's card. Jaden starts rapping, defeating Paradox's dragons. Paradox Synchro Summons Malefic Paradox Dragon. On Yugi's turn, he uses the rules of Duel Monsters that applied to his time to summon Dark Magician and "Dark Magician Girl with Big Boobies". Dark Magician Girl asks how they can talk in the movie, to which Dark Magician replies "A wizard did it". Things are going well until Paradox summons Malefic Truth Dragon. The protagonists all sing a parody of the song "Beezleboss" by Tenacious D during their last turn and defeat Paradox, apparently killing him. Yusei and Yugi decide that if anyone asks, Jaden did it. As they are saying their goodbyes and arguing over who actually won the duel, Jaden reveals that Yami will die at the end of his series. Time and space collapse and the three protagonists are warped to purgatory. Yuma Tsukumo appears yelling how "extreme" the subspace is.
After the credits, the Cybernetic Ghost of Christmas Past from the Future tells Seto Kaiba what the movie was about. When Seto asks why he wasn't in the movie, CGCPF tells him that he was never born, and that he is actually a robot. Seto realizes this is bullshit, and CGCPF says that he is Seto's true father.