Yusei Fudo had a nightmare about the Zero Reverse incident that his father created. With Yusei upset, Jack Atlas and Crow Hogan decided to have a Turbo Duel to cheer Yusei up. After driving down the highway, Paradox, who traveled back in Yusei's time, challenges Yusei to a Turbo Duel. After a few turns, Yusei tunes "Junk Synchron" with "Junk Warrior" and Synchro Summons "Stardust Dragon", but Paradox reveals a blank card and launches a beam at "Stardust Dragon", absorbing it and creating a blackened corrupt card of it into the blank card. Yusei confronts Paradox, who shows him the corrupt card, before vanishing through time again. Yusei, Jack and Crow halt their Duel Runners and look in bewilderment at the original "Stardust Dragon" card, whose illustration has just been blanked.
Yusei, Jack and Crow then started questioning about Paradox's identity at their garage, when Akiza Izinski, Leo and Luna arrived and showed the archives they found about the past. They found an old article about "Maximillion Pegasus" and "Yugi Muto", with Yusei recognizing Yugi as a legendary duelist. They also discovered a record of "Stardust Dragon" assaulting various duelists in Europe. Knowing that "Stardust Dragon" could not have existed in that era, Yusei zooms in on the article's picture to discover Paradox standing in the background of the dragons. Outside, New Domino City begins to crumble and collapse. Witnessing the destruction, Jack Atlas realized that "Stardust Dragon's" existence in the past is now changing the future, which is their era.
With the support of the other Signers, their marks begin to glow as the complete Crimson Dragon appears on Yusei's back followed by Yusei's Duel Runner glowing as well. Yusei feels himself being called by the Crimson Dragon and beckons Yusei to board his runner. With its help, a time slip is opened and Yusei begins his chase after Paradox.
In Venice, Paradox finds Jaden Yuki, who still has the powers of Yubel and The Supreme King. Paradox attacks him with "Cyber End Dragon" and "Rainbow Dragon". Jaden manages to resist by Summoning "Elemental HERO Neos" to protect him. In response, Paradox Summons "Stardust Dragon", a monster from the future, and proceeds to overwhelm Jaden (This scene is how the movie opens before changing to Yusei's nightmare of Zero Reverse). Stardust Dragon's first attack almost destroys Neos and sends the two skidding backwards into a wall.
As Paradox commands Stardust Dragon to attack Jaden again, Yusei appears with the Crimson Dragon, who takes the blows for Jaden. Paradox disappears once again.
Soon, Yusei and Jaden began to chat on a roof. Seeing Yusei's Duel Runner, Jaden gets excited seeing such a technology, asking Yusei if that was the Duel Disk of the future. He then explained that he came here because he heard that there were cards missing from duelists. Yusei explains to Jaden that Paradox is trying to change the past and that his target was Maximillion Pegasus. Jaden then used his laptop to find out an article about the event that Paradox performed that would create a major historical event. (In the English version, Jaden did not believe Yusei, which is why he opened his laptop and discovered that truth.) Jaden then checks his card, as his "Elemental HERO Neos" card turns into a blank card. As the country began to collapse, Yusei tells Jaden that they must hurry to save the world.
Yusei and Jaden then ride Yusei's Duel Runner, with the Crimson Dragon taking both of them even further back in time.
Meanwhile, in Yugi's timeline, sometime after Battle City but before the Waking the Dragons arc, Maximillion Pegasus is currently holding a tournament. The Sakiyomi Jan Bang! made a cameo as the MC of the event. Yugi and his grandfather, Solomon Muto, noticed "Stardust Dragon", "Cyber End Dragon" and "Rainbow Dragon" in the sky. Paradox then attacks the crowd with "Cyber End Dragon" and "Stardust Dragon", killing almost everyone, including Pegasus and Yugi's grandfather.
Amongst the ruins, Yugi is the only survivor against Paradox's attack. He stands up and searches for other survivors. He finds a bandanna belonging to his grandfather and cries over his death. He then sees Paradox laughing on top of a building, happy that he finally completed his mission. At that moment a crack in the space appears and the Crimson Dragon suddenly "swallows" Yugi. Then, Yugi is thrown back in time at the same place half an hour earlier. Yusei and Jaden find Yugi and explain to him what they know about Paradox to him. Yugi agrees to fight with them against Paradox to free the trapped monsters and save the world.
At the event, Jaden Summons Yubel and starts to scare the audience, so they would flee. By doing so, Yugi hopes the future is safe as Jaden regains his "Elemental HERO Neos" card. However, Paradox arrives regardless to the shock of the heroes. After Paradox took his mask off and introduced himself, Yugi asks Paradox what kind of person he is. Paradox replies that he is from a future which was destroyed by Duel Monsters. He intends to destroy the game of Duel Monsters to prevent that future from happening. Yusei tries to tell Paradox that by changing time and trying to destroy Duel Monsters, he will also erase people from the timeline as well, to which Paradox replies that it is what he is looking forward to the most. Yusei, Yugi and Jaden challenge Paradox to a 3 on 1 Duel, with a time limit of 20 minutes, before Pegasus arrives at the event and the other dimensions crumble to pieces. Jaden's eves change color as Yubel appears behind him and Yusei's Mark of the Dragon glows as the Crimson Dragon roars behind him as the two Duel Kings say their catchphrases and then Yami says to Yugi that the Duel against Paradox would be the toughest and Yugi responds by saying that they should rise to the challenge. Yugi transforms into Yami and says his catchphrase as Paradox accepts this challenge and the Duel begins.
Paradox's Duel Runner transforms into a flying type and he floats up high and the Duel begins.
Paradox declares the first move. He activates "Malefic World" that lets him put a random "Malefic" monster from his Deck to his hand instead of drawing a card during his Draw Phase. The field begins transforming into a purple atmosphere full of stars. Then, he sends "Cyber End Dragon" from his Extra Deck to the Graveyard to Special Summon "Malefic Cyber End Dragon" from his hand. He sets a card to end his turn (because in a 3-on-1 Duel, you cannot attack on the first turn). By this time, Yugi, Jaden and Yusei come to the realization why Paradox has been stealing monsters: He's using them to Summon the "Malefic" monsters, as Yugi understands that by destroying a monster's good version, Paradox can Summon their dark version.
Yusei tells everybody that despite them never fighting together before, they must work together to defeat Paradox, as Yugi & Jaden agree. Yugi then asks Yusei to take the first turn for his team.
Yusei activates "Reincarnation of Hope", which sends "Sonic Chick" and "Quillbolt Hedgehog" from his hand to the Graveyard; but on their team's second Standby Phase, they are allowed to add a monster from their Deck to their hand. Yusei then Summons "Junk Synchron" and due to its effect, he also Summons "Sonic Chick" back on his field. He then activates the effect of "Quillbolt Hedgehog" to Summon it back to his field. He then uses the 3 monsters to Synchro Summon "Junk Gardna" in Defense Position. Yugi becomes surprised by the concept of Synchro Summoning, as Jaden is just as confused by Yusei's Synchro card, but praises Yusei's play and shows his interest in the future cards. Yusei Sets 2 cards to end his turn.
Paradox adds "Malefic Rainbow Dragon" to his hand due to the effect of "Malefic World". He then sends "Rainbow Dragon" from his Deck to the Graveyard to Special Summon "Malefic Rainbow Dragon" from his hand. Jaden then becomes angry since Paradox is using Jesse's card. Paradox attacks "Junk Gardna" with "Malefic Rainbow Dragon", but Yusei activates the effect of "Junk Gardna" that switches "Malefic Rainbow Dragon" to Defense Position, thus stopping the attack. Paradox then attacks "Junk Gardna" with "Malefic Cyber End Dragon", this time destroying it and inflicting Piercing Damage to Yusei's Life Points. Yusei felt the real damage that Paradox did to him, but not before activating "Junk Gardna's" 2nd ability, which switches Paradox's other monster in Defense mode and "Miracle's Wake", reviving his "Junk Gardna". Yusei apologizes for losing some Life Points, but Yami and Jaden insisted that Yusei did a good job, stopping the assault of both monsters. Paradox then Sets a card and ends his turn.
As Jaden's turn begins (his theme song plays in the Japanese version), he asks Yusei if he may borrow "Junk Gardna". Yusei agrees, as Jaden activates "Polymerization", fusing his "Elemental HERO Neos" with Yusei's "Junk Gardna" to Fusion Summon "Elemental HERO Neos Knight". The ATK of "Elemental HERO Neos Knight" increases by half the ATK of "Junk Gardna", making it 3200. Because of the other effect of "Elemental HERO Neos Knight", it can attack twice during the same Battle Phase. Thus, Jaden attacks Paradox's "Malefic Rainbow Dragon" and "Malefic Cyber End Dragon" with "Elemental HERO Neos Knight". Paradox activates "Malefic Tune", allowing him to draw 2 cards. Jaden Sets four cards to end his turn.
Paradox adds "Malefic Stardust Dragon" to his hand due to the effect of "Malefic World". He then sends "Stardust Dragon" from his Extra Deck to the Graveyard to Summon "Malefic Stardust Dragon". Yusei then became shocked to see that his ace monster became corrupted and in the English dub he yells at Paradox, calling him a snake and is horrified at what has been done to his card. Paradox then Normal Summons "Malefic Parallel Gear" and tunes it with "Malefic Stardust Dragon" to Synchro Summon "Malefic Paradox Dragon". Yusei is stunned by this, to which Paradox says that he is not the only one who could Synchro Summon. He activates its effect, Special Summoning "Stardust Dragon" and decreasing the ATK of Jaden's "Elemental Hero Neos Knight" by 2500. Paradox attacks "Elemental HERO Neos Knight" with "Malefic Paradox Dragon", but Jaden activates "Hero Barrier", negating the attack. Yugi and Yusei praise Jaden for that move, but Paradox activates "Malefic Claw Stream", destroying "Elemental HERO Neos Knight", but Jaden activates "Elemental Mirage", resurrecting "Elemental HERO Neos Knight" with its original ATK (2500). He explains to Yugi and Yusei that he did this to ensure that there was at least a monster on the field by Yugi's turn. Because of the effect of "Malefic Paradox Dragon", the ATK of "Elemental HERO Neos Knight" is reduced to 0. Paradox Sets 2 cards to end his turn.
As Yugi's turn began (his theme song plays in the Japanese version), he adds "Dark Magician" to his hand due to Yusei's "Reincarnation of Hope". Paradox knew that he would try to go for the "Dark Magician". Yugi activates "Ancient Rules", which allows him to Special Summon it. The Dark Magician, however, is still affected by the effect of Malefic Paradox Dragon, reducing its ATK to zero. Jaden gets excited seeing Yugi's ace card, while Yusei remembers based on the archives, the Dark Magician is Yugi's ace monster. At this point, Yusei asks Yami to destroy Stardust Dragon, since Malefic Paradox Dragon's effect will prevent them from launching an attack. Yugi then activates "Bond Between Teacher and Student", which Summons "Dark Magician Girl" to his field. Yami then activates "Magic Gate of Miracles", which lets him take control of one of Paradox's monsters and which Paradox assumes it is his "Malefic Paradox Dragon". In response, Paradox chains "Malefic Force", which protects his "Malefic Paradox Dragon" from Yami's card effects. Yami then smiles claiming his true target is "Stardust Dragon". Now Yusei gets his "Stardust Dragon" back on his field. Jaden then praises Yami for this, noting that Yami never wanted Malefic Paradox Dragon in the first place. By doing so, Malefic Paradox Dragon's effect is negated, thus returning the Dark Magician & Elemental Hero Neos Knight's ATK to their original amount. Yami then activates "Dark Magic Twin Burst", combining his two monsters' ATK together, raising the ATK of "Dark Magician" to 4500. He attacks and destroys "Malefic Paradox Dragon", resulting in Paradox losing 500 Life Points. Paradox then grins, claiming that these desperate moves change nothing. Yugi disagrees, mentioning to Paradox that he had two monsters and now he has none. Paradox mentioned that they only created the path for the Summoning of a powerful monster and activates "Malefic Paradigm Shift", which Summons "Malefic Truth Dragon" to his field when his "Malefic Paradox Dragon" is destroyed. This costs Paradox half of his Life Points to activate (Paradox: 1750 Life Points). Paradox then fuses with his new monster and everyone is amazed to see such a gigantic monster. Yugi then Sets 2 cards face down and ends his turn.
By now, time has run out as Pegasus is about to arrive, but cannot land his helicopter due to Malefic World still being in play. Back in New Domino City, everybody is watching their dimension collapse but Jack knows that Yusei still has a chance.
Paradox then starts his turn. He plays "Malefic Selector" to remove "Malefic Parallel Gear" and "Malefic Cyber End Dragon" from play to add "Malefic Blue-Eyes White Dragon" and "Malefic Red-Eyes Black Dragon" to his hand. Paradox then sends both "Blue-Eyes White Dragon" and "Red-Eyes Black Dragon" from his Deck to the Graveyard to Summon "Malefic Blue-Eyes White Dragon" and "Malefic Red-Eyes Black Dragon".
Yugi is shocked that the "Red Eyes Black Dragon" & "Blue Eyes White Dragon" have become Malefic monsters as well. Paradox then attacks "Dark Magician Girl" with "Malefic Red-Eyes Black Dragon". At that point, he also mentions Malefic Truth Dragon's ability: If a Malefic monster destroys one monster, the other monsters are destroyed also. Jaden then activates Yugi's "De-Fusion", sending Elemental HERO Neos Knight back to the Extra Deck and Summoning his "Elemental HERO Neos" and Yusei's "Junk Gardna". Yusei then uses the effect of "Junk Gardna" to switch "Malefic Red-Eyes Black Dragon" to Defense Position, thus canceling its attack. Yugi praises both Jaden and Yusei for this impressive display of teamwork but then Paradox then attacks "Dark Magician" with "Blue Eyes White Dragon" and destroys it, costing Yugi, Yusei and Jaden 500 Life Points. He then activates the effect of "Malefic Truth Dragon" which would destroy all of Yami, Jaden and Yusei's monsters, but Yusei activates the effect of "Stardust Dragon" to negate the destruction effect of "Malefic Truth Dragon" and destroy it. However, Paradox activates the effect of "Malefic Truth Dragon" which removes from play his "Malefic Rainbow Dragon" and negates the effect of "Stardust Dragon". He then attacks "Elemental HERO Neos" with "Malefic Truth Dragon" and thus activating its effect again, destroying "Dark Magician Girl" and "Junk Gardna". Also, for every monster destroyed, Malefic Truth Dragon inflicts 800 damage. Yami, Jaden and Yusei's Life Points are all reduced to 500 as all 3 of them are pushed back by the explosion. Paradox then activates "Malefic Divide", Special Summoning "Malefic Stardust Dragon" from the Graveyard. He then orders it to unleash its fury so that Duel Monsters will perish forever. Yusei falls to his knees, saying that everything is lost and the future is doomed. Jaden tells Yusei not to surrender reminding him that they have a "secret weapon" on their side. Yugi also tells Yusei that other than Paradox, they believe in Duel Monsters. To show him what he means, Jaden activates "The Flute of Summoning Kuriboh". The effect of "Flute of Summoning Kuriboh" allows Yami to add "Kuriboh" to his hand. Yami then discards "Kuriboh" to reduce the Battle Damage to 0. Paradox ends his turn, but not before "Malefic Stardust Dragon" gets destroyed by the effect of "Malefic Divide" and the original "Stardust Dragon" gets Summoned back to Yusei's field due to its ability. Yami then tells Yusei that no matter which era he is in, his friends will always be supporting him.
Yusei gets up, as Yami & Jaden tell Yusei to end the Duel, as they promise to aid. Yusei activates "Stardust Mirage", Special Summoning all monsters that Paradox destroyed during this turn. This brings back "Dark Magician Girl", "Dark Magician", "Elemental HERO Neos" and "Junk Gardna". Paradox is shocked, as all the monsters previously destroyed in his turn are Special Summoned back to their field. Yusei then draws a card to start his turn, as Jaden then activates "Neos Spiral Force", doubling the ATK of "Stardust Dragon" to 5000. Yami then activates "Dark Spiral Force". This then doubled Stardust Dragon's attack again to 10000. Yusei attacks "Malefic Truth Dragon" with "Stardust Dragon" and the combined efforts of "Dark Magician" and "Elemental HERO Neos", winning the Duel and restoring peace. Paradox is destroyed by the attack and is never to be seen again. Pegasus is finally able to land and arrive at the event.
After the Duel, Yusei thanks Jaden and Yami and hopes to meet them again, as Yami looks down from the rooftop towards the event where Pegasus is among the crowd. Yami gives a friendship speech and Yusei and Jaden return to their respective timelines. Back at New Domino City, everybody comes running to Yusei as Yusei himself looks at the sky and hopes to protect his future so that one day, he can meet Jaden and Yugi/Yami again. In the English version, he also says that the true magic of Duel Monsters isn't in the cards, it's the bonds we forge because of it.
- Yuya Miyashita as Yusei Fudo
- KENN as Jaden Yuki
- Shunsuke Kazama as Yugi Muto & Yami Yugi
- Takanori Hoshino as Jack Atlas
- Shintaro Asanuma as Crow Hogan
- Ayumi Kinoshita as Akiza Izinski
- Leo Ai Horanai as Leo
- Yuka Terasaki as Luna
- Kappei Yamaguchi as Lyman Banner
- Hiromi Tsuru as Yubel
- Tadashi Miyazawa as Solomon Muto
- Jiro Jay Takasugi as Maximillion Pegasus
- Kazunari Kojima as Dark Magician
- Yuki Nakao as Dark Magician Girl
- Atsushi Tamura as Paradox
- Greg Abbey as Yusei Fudo
- Matthew Charles as Jaden Yuki
- Dan Green as Yugi Muto & Yami Yugi
- Ted Lewis as Jack Atlas
- Tom Wayland as Crow Hogan
- Bella Hudson as Akiza Izinski & Dark Magician Girl
- Eileen Stevens as Leo, Luna & Yubel
- Wayne Grayson as Solomon Muto & Lyman Banner
- Darren Dunstan as Maximillion Pegasus
- Michael Sinterniklaas as Dark Magician
- Sean Schemmel as Paradox
- Several times during the Duel, fewer cards are seen in someone's hand than there should be.
- When Yusei revives "Junk Gardna" with "Miracle's Wake", a face-down card is seen on both sides of it when there should've only been one.
- When Jaden is about to attack "Malefic Rainbow Dragon", the original "Rainbow Dragon" is seen on Paradox's Duel Disk instead of its "Malefic" version.
- When Paradox Synchro Summoned "Malefic Paradox Dragon" and it appeared on the field, "Elemental Hero Neos Knight" is not on the field but its card is seen on *Jaden's Duel Disk after "Malefic Paradox Dragon" is Summoned.
- When Yusei revives all of his team's monsters with "Stardust Mirage", the DEF of "Junk Gardna" is mistakenly shown as 2500 instead of 2600.
- Pegasus is shown with the Millennium Eye, despite the movie taking place after he lost it at Duelist Kingdom, although this may just be an animation mistake.
- In the English version, when Yusei activates "Stardust Mirage" the underside of Jaden's face-down is also "Stardust Mirage" instead of "Neos Spiral Force".
- In the English version, when Yugi uses the effect of "Kuriboh" to block the attack of "Malefic Stardust Dragon", he calls it "Stardust Dragon" instead of "Malefic Stardust Dragon".
all information on the Yu-Gi-Oh! 5D's movie came from http://yugioh.wikia.com/wiki/Yu-Gi-Oh!_3D_Bonds_Beyond_Time