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1* How is [[spoiler:the Ring still evil and able to corrupt people when Zorc and Yami Bakura are gone?]] The manga implied the reason it [[spoiler:burned the unworthy to the bone was because of Zorc/YB's evil, and even if Aigami and Mani are powerful enough to be protected from dying, it still turned them evil and tried to make them kill Ryou, who was the Ring's destined host in the manga]]. While [[spoiler:Ryou]] wasn't its ''only'' master, as evidenced by [[spoiler:Mahad, Mana, and even Yugi]] (plus Kaiba in ''VideoGame/YuGiOhMonsterCapsuleGB'' and Alexander the Great in ''Anime/YuGiOhCapsuleMonsters''), he was the only one who ''wore'' it in the present day up til now.
2** The movie is manga canon, so Capsule Monsters isn't relevant. There's been estimations that perhaps Mahad and Mana trained to resist the Ring's darkness, but that's entirely guesswork.
3** Another possibility is that it became corrupted ''after'' [[spoiler:Mahad]] lost it to [[spoiler:Bakura.]]
4** In the manga Mahad speculated it was the ''previous'' Ring priest's darkness that made the Ring so evil, but that could be another offset of Zorc's power so it's hard to say for sure. Mahad also used most of his own magic to resist the Ring's darkness, which prevented him from fighting at full potential.
5** Another possibility is that Zorc and Bakura being in the Ring too long tainted it with evil, but without Zorc/Bakura actually being in there.
6** [[RuleOfThree Yet]] ''[[RuleOfThree another]]'' [[RuleOfThree possibility]] is that Zorc/Yami Bakura infused a piece of their soul into Diva himself on the night Shin was killed, only manifesting once again when the Millennium Ring fell into Diva's possession. In the dub Dark Diva states some oddball things like "Diva is no longer in control; I am. His fear invited me into his soul. He has saved me!" and, "Shin is no longer my master! That is why I did away with him!" Diva wouldn't denounce Shin as his master nor was he the cause of his death. The only other entity present that night who did away with Shin ''and'' had the ability to infuse parts of his soul into objects was Yami Bakura.
7* How did little Bakura get home from Egypt after [[spoiler:Yami Bakura killed Shadi, his father, and everyone else there?]]
8** Possibly other family members or child services.
9** He simply wasn't killed. He was mentioned in the manga as being alive.
10* If [[spoiler:Mr. Bakura was killed by the Ring]] how did the manga's Millennium World happen? It worked out the way it did because he was the curator of the museum, allowing Bakura to build the diorama there.
11** It's easily explained by the museum curator actually being an adoptive father.
12*** That wasn't the case in either guidebook for the manga or the anime, though, and him being an adoptive father opens up a bunch of new questions/plotholes, like how did it happen and how long ago, was Ryou's original last name Bakura or did they share the name, and why he and the first Mr. Bakura have the same occupation. (A manga guidebook and the anime said Ryou's father is always away on archaeological business and owns the museum, which is what DSOD's Mr. Bakura also does.) According to [[http://sliferthewhydidigeta.tumblr.com/post/127734965026/shinhoroko-interviewer-out-of-the-many this]] interview Takahashi said he was forgetting what happened in the manga so the out-of-universe explanation could just be 'the writer forgot what he wrote.'
13*** Whether or not Ryou's father died is ambiguous in the subbed movie. It's only confirmed in the dubbed movie.
14** It's also possible that Bakura's father never died, and just got attacked, like the rest of the kids, while Bakura's "person he lost that day" could have been Amane Bakura, his sister, or his mother.
15* What was up with the parallel Earths disintegrating at the start of the movie? Was it a side-effect of Kaiba's research or Aigami's powers?
16* How did [[spoiler:Sera, Aigami, and Mani]] get back to Egypt at the end after they [[spoiler:lost their powers]]?
17** Per airplane, I guess? I mean, Yugi is a NiceGuy whose closest FriendlyEnemy owns a world-influential MegaCorp; handing out some plane tickets should be the smallest of issues.
18* How does Dimension Dueling work?
19** You can basically Normal or Special Summon monsters from your hand as much as you feel like, though neither player takes damage from battles involving Dimension Summoned monsters. However, players take effect damage equal to their monster's ATK or DEF when they are destroyed, depending on their battle position at the time. There's also a rule where you can determine the ATK and DEF of a Dimension Summoned monster that's lower than its original value, but no one does that in the film.
20** In addition, if you Tribute or use them for Fusion the newly summoned monsters also count as being Dimension Summoned.
21** Also either Phases don't exist or you can Summon during the Battle Phase.
22* Kaiba's LP counter stopped at 100 before the duel ended, with a slight grin on Kaiba's face. What was his face-down card, before the duel interrupted?
23** Polymerization. Kaiba set it the turn before as a bluff, he had no counterplay to Yugi's Final Gaes trap. The smirk was most likely him accepting defeat.
24** According to [[http://yugipedia.com/wiki/Yu-Gi-Oh!_The_Dark_Side_of_Dimensions#Yugi_Muto_vs._Seto_Kaiba this]] it wasn't anything specific, though his hand did contain Polymerization. It's possible it'd be a trap related to Polymerization in some manner, but since the duel was interrupted we'll never really know.
25** [[https://www.youtube.com/watch?v=QnCTdNnILp0 This guy]] did a turn by turn breakdown of the Duel, and it seems it was indeed "Polymerization". The reason for his grin is still up for interpretation, but it likely was him accepting defeat and acknowledging Yugi as a WorthyOpponent.
26* When Kaiba [[spoiler: went to the afterlife to duel Atem]], why was there darkness flaking off of him? Similar to during the [[spoiler: tag duel with Yugi against a corrupted Aigami.]]
27* When Dark Magician Girl was summoned, why didn't she get the 300 ATK boost from Dark Magician in the graveyard?
28** Apple Magician Girl and Lemon Magician Girl share the same movie effect; when they're attacked they can either special summon a lower level spellcaster monster from the hand OR special summon a higher level spellcaster monster with their effects negated, then halve the attack of the attacking monster and redirect it. Since Dark Magician Girl is level 6 that means her effect was negated.
29* Why does everyone in this movie start with 8000 LP? In the anime, every duelist starts with 4000 after Duelist Kingdom. And this is the case for both the anime set before the movie (Duel Monsters) and for the anime set after the movie (from GX onwards).
30** The movie only follows the manga, while ''GX'' and all the others follow the anime. Also, this isn't the first time Duel Monsters has had its gameplay modified.
31* What happened to the Eye, Rod, Necklace, Scales, and Key? If the Puzzle and Ring were unearthed someone may have picked those up as well.
32* According to [[https://68.media.tumblr.com/dd68deff5958394d23f1552571437ced/tumblr_okqttioFpN1u76hl0o3_500.png this manga panel]] as long as Bakura doesn't ''wear'' the Ring it can't do any harm, but in this movie the Ring corrupts several people without being worn, and in Aigami's case without even touching it.
33** We've seen another manga scene [[https://i.imgur.com/96ZvxjB.jpg depicting Yugi simply touching the Millennium Puzzle while it's not around his neck and Yami appearing.]] We also can't be sure if that is really Bakura saying that, as Yami Bakura can do a damn good impersonation of his host. For all we know, that statement might not be true in the slightest.
34* Everything about the Plana is confusing, especially ''why'' Shadi would give them the powers under such conditions. It makes the end of the manga/anime a NiceJobBreakingItHero moment since the Pharaoh leaving was what caused the whole movie to happen, not only with Kaiba's plotline to assemble the Puzzle, but also Aigami's escalating war. Atem ''had'' to return to stop the Plana since him leaving started it, despite the movie ''also'' enforcing the idea that he ''couldn't'' return and everyone had to move on, including Yugi and Kaiba.
35** The Plana is confusing, but there's a possible explanation. Shadi gave them their powers with the intent of having them make the world a better place. If Seto hadn't have tried to resurrect the Pharaoh, Aigami probably would have tried to use his powers for their original intended purpose. Additionally, if Aigami hadn't tried to stop Seto then probably nothing would have happened. Yugi would have solved the Puzzle at Seto's request, but Atem would have no reason to return and Seto would have had to accept it then (probably). Perhaps Shadi gave them the powers under the condition of the Pharaoh leaving for two reasons: 1. The Pharaoh would no longer be around to defend humanity from magical threats himself, and 2. With the magic of the Items more or less sealed and that conflict over, humans could progress using magic with no bad origins (the Kul Elna massacre). The Pharaoh's return ridding them of their powers is perhaps a failsafe - if there was a threat so great that the Plana couldn't handle it, or if the Pharaoh needed to return, that would show that the Plana weren't working out as intended, so their powers should be removed and people would have to improve the world without magic. If we assume that the Pharaoh returning is only possible if the Puzzle is reassembled, that would mean someone was messing with the Items again. The magic from the Items might be a greater threat than the Plana can handle (Atem did p*wn Monster!Aigami pretty easily, though that might be because of his own power and not the Puzzle), so the Pharaoh returning might rid them all of their powers again to protect people from the Millennium Item magic. He does send the Puzzle to the Afterlife at the end of the movie, suggesting all Millennium magic is now gone for good. Tl:dr, Shadi probably intended for the Plana to do good but in making Aigami afraid of the Pharaoh's return, it accidentally ended up leading to Aigami helping cause the Pharaoh's return.
36* Where did the Quantum Cube come from, how was it made, and why did Shadi use it instead of the Millennium Key or Scales? As an eighth Millennium Item, was it made in the same way as the others?
37* If the Cube's powers activated upon the Pharaoh's departure, why was Shadi able to use it before then?
38** Because it was before Yugi completed the Puzzle and woke him up.

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