In Yu-Gi-Oh! 3D: Bonds Beyond Time, there is a scene where Paradox appears and kills Pegasus, Sugoroku, and thousands of innocent fans in the process of trying to end Duel Monsters, but I have no clue what time period it takes place in. I figured it took place between two miscellaneous arcs in the story, but there isn't any evidence supporting that. I was mostly wondering because he somehow used Atem's form despite Atem being freed. If anyone has any ideas, please let me know.
The event takes place sometime after Battle City but before the Waking the Dragons arc. It is important to point out that the production of this movie overlooked many errors.Some of which confused many fans of the franchise.
1: Several times during the Duel, fewer cards are seen in someone's hand than there should be.
2: 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.
3: 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.
4: 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.
5: 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.
6: 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.
7: In the dub, when Yusei activates "Stardust Mirage" the underside of Jaden's face-down is also "Stardust Mirage" instead of "Neos Spiral Force". In the dub, 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".