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Narrative
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Yu-Gi-Oh GX
Darkness and Zorc are related.
They look alike, they have similar motives, they both use realtively innocent hosts who (using season 0 for Bakura) attract many girls, they each disappear in the thirdish season (Waking the Dragons and Yubel) and reappear as main villan as the forth, they each have two hosts (Thief King Bakura and Little Bakura for Zorc, Fujiwara and Fubuki for Darkness). They're each epic and this trooper is a fangirl of Zorc and thinks Darkness is cute.
The Abandoned Dorm incident was a semi-failed attempt to recreate the Egyptian God Cards and Millennium Items.
The original Millennium Items needed 99 human souls to be created, and while the exact number of students missing was never established, it's big enough to force a cover-up. Also, note that the Shadow Charms bear some resemblance to their Millennium Item counterparts (for instance, the Millennium Eye and Shadow Eyepatch), each with an unspecified power. Then, there's the similarity in both look and effect/strength of the Sacred Beast Cards and the Egyptian Gods; and dueling energy is needed to reacquire them. (The Egyptian Gods and Millennium Puzzle required a duel for them to legally change hands; the Sacred Beasts need all seven Spirit Keys to be won by a challenger in a duel to unlock their hiding place). Finally, replicas of the hieroglyphs that were required to unlock Pharaoh Atem's memory (also using the Items and Egyptian Gods) are on display at the Abandoned Dorm, and there's a hidden dueling arena in a cave underneath the Dorm. This all seems to point to an attempt by Kagemaru to recreate the Millennium Items and Egyptian God Cards. It only worked in part; the lack of demonstration of the Shadow Charms' powers indicates that they - like the Sacred Beasts - aren't as powerful as the originals.
Johan Anderson is the half-brother of Yuki Judai and Marufuji Shō/Marufuji Ryo.
Johan's look, personality, and dueling strategy are all similar to Judai's, but he has teal hair and some physical characteristics like Sho and/or Ryo. Plus, we know nothing about Johan: not his age, not who his parents are, nothing. And his Face Heel Turn after his possession by Yubel gives him a revamped look like Hell Kaiser Ryo with the same flippant disregard for the opponent that Hell Kaiser had. Plus, we know that Judai's parents were never home when he was a kid. Sho seems to stay at the Academy with Judai during the holidays, possibly indicating the same, giving their parents enough time to have an affair and keep Johan's existence a secret until they could give the baby up for adoption. Finally, there's Johan's and Judai's feeling that they met somewhere before their initial meeting; close relatives do seem to have a knack for sensing when their siblings are near. They also have a Ho Yay Love Triangle going, so this could lead to some... interesting developments once the truth comes out.
Fubuki Tenjoin is a flaming homosexual; Darkness is the embodiment of his attempt to suppress that and become a Ladies' Man, brought to life by his Shadow Charm.
First, he's obsessed with the pop idol shtick, so secretly-gay boy band jokes apply. Second, he's ridiculously showy even with his obsession. Third, despite his parading to the girls, he has yet to seduce any of them and has hidden from them when they started stampeding towards him - something that a true Ladies' Man would never do. He gives lousy dating tips to the heterosexual Manjyome, showing his lack of understanding of women.
So, why is Darkness his repressed sexual nature come to life? Simple: he takes all the above and strips away the facade of woman-wooing, making them manlier. Also, during his duel with Hell Kaiser, he makes two contradictory statements about his Superpowered Evil Side: he says that it'll always be a part of him, but he later says that it's gone and will never come back. Note that the second statement is made under duress after Hell Kaiser questions his competence with his alter-ego's deck, wondering if it was him or it that was calling the shots. This could be Fubuki's acknowledgment that he's homosexual, but denial that he's ineffectual because of it. Plus, every other alter-ego in Yu-Gi-Oh (except the ones that were another being entirely possessing the person's body) had been created from repressed emotions brought forth via a magical item (Marik and Yami Marik, Judai and Supreme King Haou, etc.). Fubuki was given one half of the Shadow Pendant, so...
Judai is destined to finish Yugi Mutou's last task: sealing up Zorc and the Shadow Realm/Duel Monsters Realm forever.
First, why else would Yugi give Judai a Light-Attribute version of Kuriboh, one of his favorite monsters (and the ka of the Nameless Pharaoh)?
Also, before and during Yugi's stint as the vessel for the Pharaoh, the only way for the Duel Monsters to become "real" was through Shadow Games. Now, several duelists have the ability to see Duel Monster spirits, and all that's needed to summon them is a specific holiday celebration or incantation that anyone can perform. It is also way too easy for Judai and the gang to use their Duel Monsters to reopen the portal back to the Duel Monsters dimensions in Season 3, hinting that the boundaries between the real world and the Duel Monsters dimensions are at their weakest. It's no coincidence that Yugi would give the light version of his Kuriboh to a kid that not only can see said Duel Monsters, but also has dueling prowess equal to or surpassing his own, especially once he gained his status as Supreme King Haou.
So why doesn't Yugi try and fix the problem himself? Because, despite popular belief, he didn't destroy Zorc during Memory World; he just resealed the fiend and is too busy with keeping that monstrosity at bay to do anything else. (Hence why he was gone from his Grandpa's for so long.) Yugi could sense the potential in Judai and gave him Winged Kuriboh as a "passing of the torch" to complete his mission and keep the two worlds separate. The final nail in the coffin shows up in Season 4; right after the gang's romp through the Duel Monster Universe triad, Kaiba's Hard Light duel disk imaging devices start malfunctioning, indicating that the veil between worlds is thin enough for the monsters to emerge without such assistance.
Taniya is the Duel Monster Scar-Eyed White Tiger.
It's already been established in the Seven Star Assassins arc that the Shadow Charms can bring Duel Monsters to life in the real world (as the Eyepatch did for Don Zaloog). Once she was beaten, Taniya transformed into a white tiger looking similar to Scar-Eyed. Also, she pops back up in the second of the Duel Monsters dimensions in season 3; if she wasn't a Duel Monster, but a regular tiger, then how did she get there? Then there's her "pet" tiger that looks exactly like Amazoness Tiger and could be the monster come to life...
The Abandoned Dorm wasn't an alternate Obelisk Blue boy's dorm, but a specialized dorm for students who could see Duel Monsters spirits and had other duel-related special powers.
The dorm had only been abandoned for a year before Season 1. It's not impossible, given Kaiba's access to massive amount of funds, but it's unlikely that a brand-new boy's dorm would be constructed within that time. Plus, there's the relics of the ancient ancestry to Duel Monsters in the abandoned dorm (which no other dorm has, and likely no other dorm will ever have, given Kaiba's refusal to believe such nonsense) and its own ritualistic Duel Arena (again, something none of the other dorms have). Plus, if we're to believe that the dorm was abandoned because of an attempt to recreate the Millennium Items, having it be home to the school's more preternatural students makes sense; sacrificing such people would give more power to the Items. Fubuki was called there because of his connection to Fujiwara (who has his own Duel Spirit partner, the monster Honest) and the ritual Fujiwara performed to bring back Darkness.
The reporter who was interested in the Abandoned Dorm incident was paid off or killed by Kagemaru to keep the story secret.
He swore to the gang that he'd help them find out the truth behind the incident, and then vanished with no word on whether he got the story out. Considering how hard the school tried to keep the incident under wraps, it's likely he was silenced with either money or a bullet to the head to keep the truth from being leaked.
Duel Academia is an orphanage where the kids are kept happy by having them play a collectible card game all day.
First of all, Duel Academia is owned by Seto Kaiba, who is himself an orphan; in the original series, he did seem to have a soft spot for orphans, though he would never admit any such weakness. Second, the only parent we ever see is Hayato's father; given how he feels about his son, it's not impossible that he disowned Hayato after he failed his exams for the second time. Third, after Fubuki returns from the Shadow Realm, neither he nor Asuka make any visible effort to contact their parents about his return. You'd think that they'd want to know that their missing son had reappeared. (Granted, the school is engaged in a massive cover-up about the missing students, but how hard is it to send an email?).
Judai is the reincarnation of Yoh Asakura from Shaman King.
In Shaman King, when Yoh was reincarnated, his soul was split in two. One became Yoh, the other became Hao. In Monster World, when Judai becomes an evil overlord, he goes by the name Hao. Evidently, Yoh's and Hao's souls were recombined some time after their deaths and returned to Earth as Yuki Judai, but remained in conflict; Yubel was able to force Hao to the surface.
The original Yu-Gi-Oh is a Show Within A Show on Neon Genesis Evangelion, and GX is another Instrumentality-induced fantasy imagined by Shinji Ikari.
Shinji, the ultimate Unlucky Everydude Non Action Guy in a painful, Deconstructed shonen universe imagines himself as a popular, talented, fearless, perfect, ultimate, too-good-for-words hero in a classic shonen series. He doesn't get the least bit nervous around Asuka, and Rei is an emotional, energetic, spunky young admirer of his. But, as Shinji rejected Instrumentality for the real world, the fantasy started to wear thin. The characters he imagined all started disappearing, and Judai's Hidden Depths were revealed as his own world and psyche started falling apart.
EVERYTHING in Season 4 is a hallucination by Judai after his fusion with Yubel, and/or the fusion/destruction of reality as he knows it.
Nothing so far in Season 4 makes sense; not Trueman, not Yusuke Fujihara/Honest, not the punk Psycho Style duelist who wants to crush the Cyber Legacy, none of it. Worse yet, the deeper we get into the season, the more confusing things get. They don't explain why the Duel Disks were acting up in the season's beginning, they barely explain Darkness' connection to the Abandoned Dorm (and the Dorm was destroyed before anything else could be divulged about the incident that happened there that Kagemaru was involved in), they don't bother to explain how Hell Kaiser Ryo survived his "death" last season and returned to Duel Academy, Honest's part in everything was never touched upon after he fused his soul with Judai... and Trueman has nebulous plans that seem to involve molesting disgruntled little boy duelists to negate the existence of all citizens in Domino City and Duel Academy. The only thing that can possibly explain this Mind Screw of a season is that Judai failed to cure Yubel's madness after they fused at the end of Season 3, became infected by it, and is slowly going irrevocably insane.
That, and/or his fusing with Yubel didn't prevent all the dimensions from fusing into one and becoming destroyed, as he hoped it would. His Heroic BSOD has deepened into pure psychosis from the aftermath and his knowing that, in the end, he couldn't save anything.
Kenzan lied about the origin of his dinosaur DNA.
Fossils are formed when organic material decomposes, and the remaining void is filled with minerals. To overly simplify things, a fossilized bone isn't a bone, it's a rock in the shape of a bone. Yet Kenzan claims that his broken leg was repaired using a dinosaur fossil. So what's with the Hellish Pupils?
Kenzan is a vat-grown hybrid clone. He and his ilk (dinosaur DNA is just the latest in a long line of human-animal hybrids) are grown as genetically engineered soldiers to be sold to the highest bidder in the event of a future war. Kenzan managed to escape the clone factory in his youth and successfully infiltrated human society. He now makes up crazy stories about the origin of his strange eyes and abilities to throw off suspicion. Despite all this, he still manages to be one of the happiest and most mentally balanced characters of the cast; this demonstrates just why his Tarot card is Strength.
Misawa and Taniya did a lot more than "dueling all night," If You Know What I Mean.
Seriously — what else are you going to do with someone bound to be your husband for only one night? The screams during the night, the PTSD-esque withdrawal the day after, the overwhelming desire for acceptance the next season and his ceasing to be a self-proclaimed Celibate Hero... something traumatic happened that night. Clearly, he lied when he told the others that they spent the night dueling. (Wouldn't you if you were him?) His pleasant demeanor around her in Season 3 only makes the implications worse.
And Misawa wasn't the only one who got spanked by a Duel Monster in the series...
Take a look at Judai's severe change in character post-Yubel soul fusion, then remind yourself that the main goal of Yubel for the third season was to make Judai its love slave and "convert" him to its form of sadomasochistic love. Then remember that Yubel admitted to orchestrating Judai's transformation into Supreme King Haou. And poor Asuka never suspected a thing...
The entire cast (minus Judai) is slowly being replaced or bumped off.
First it was Misawa staying behind to hang out with Taniya; then it's Asuka choosing to study abroad after she can't get into Judai's pants; then Sho takes over the role of Kaiser from his nearly-dead brother; and now Manjyome is screwing up Edo's career as a professional duelist and taking his place. As the fourth season is the graduating year for all the characters, this might be justified as an example of how old school friends go on with their separate lives after school ends. But this sudden push to get all of the old characters out of the picture is too blatant to be coincidence.
Jun Manjyome's mother died in childbirth.
Jun's older brothers put pressure on him to uphold the family name - not his parents, who should be more concerned about stuff like that. When he runs away and isn't seen for three months, his brothers are waiting for him when he returns to the Academy. No parents. In the beginning, it's only his brothers he wants to please, not his parents. It's his brothers' help he doesn't want to rely on to become a pro, not his parents, who would logically be the ones with the money and connections in high places - if they were alive.
Conclusion: they're not around, out of the picture - dead. After the Manjyome brothers become estranged, Jun still has an unlimited supply of money to spend on things like building his own private dormitory with a jacuzzi; clearly, he's living off a trust-fund. And why else would his older brothers despise him so much, even when he was a top-ranker in Obelisk Blue? They blame him for their mother's death (or so every other Fan Fic about their childhood says).
Season 4 was purposely cut short to cover problems on the set.
Many coincidences seem to point to this: first, unlike the other three seasons (which went from February to October), the fourth season is shutting down by March/April, half that time. Also, its replacement, Yu-Gi-Oh The 5D's, and its cards are being pushed awfully hard, with the first set of the new show coming about the same time the anime debuts - which means the GX group of card sets (from The Lost Millennium to Light of Destruction) is a full two or three sets shorter than the original anime's group (from Legend of Blue-Eyes White Dragon to Flaming Eternity); the missing three sets would've filled the gap had GX continued as scheduled. There's also the nonsense of the fourth season's premise: nothing about antagonists Fujiwara's or Trueman's motives for their actions (or their actions themselves) makes sense; the suddenness of minor villain Darkness rising up to be a big bad is equally puzzling; and many loose ends from previous seasons (like what really happened in the Abandoned Dorm incident, of which we know nothing except that Darkness had very little to do with it) remain unresolved. It's very likely that, had the show went on, Darkness would not have been the final Big Bad; he is only because the writers had to rush to get the show some closure after it was cut in half. Finally, there have been rumblings that the voice actor for Yuki Judai was demanding more money for his performance in the fourth season, money that for whatever reason the producers refused to shell out. All this seems to indicate that something happened behind the scenes to make the producers want to cancel GX for good and use the new series to defuse the backlash.
Everything from Season 4 happened only in Judai's head
Yubel is a Magnificent Bastard of the highest order. Judai, upon fusing with Yubel (her real goal, don't forget), became trapped inside his own mind, living out an elaborate fantasy while Yubel took control of his body and quietly subjugated him. His sudden appearance in a desert marked the completion of this process, and "Banner" is a shade of Yubel intended to keep Judai under control.
Alternatively, everything from the first appearance of Rainbow Dragon onwards didn't happen
...and both Judai and Johan are trapped in the Yubel card, along with the monster herself. As above, everything from there is a fantasy cooked up by Yubel to suppress Judai.
The whole of Judai's duel against Yugi was a hallucination
How else do you explain Judai going back in time, time stopping for his and Yugi's duel, and the duel ending with no conclusion, only for Judai to randomly be in a desert with Pharaoh/Daitoukouji randomly in his bag with a letter from home?
Judai isn't to blame for losing his friends and turning evil in the second half of the third season.
Think about it: Yubel's entire spiel was to make life miserable for Judai, done specifically by targeting his friends for attack after attack, but never attacking Judai directly. Judai didn't turn evil until after his friends were all captured and killed by Brron, Mad King of Dark World - a servant of Yubel specifically sent to rile Judai up and turn him evil. Had his friends stayed behind like Judai asked them to, they wouldn't have been captured and "killed" by Brron, and Judai wouldn't have suffered from it enough to turn evil. In other words, Yubel planned on Judai's friends to come with; if they hadn't, her plans would've fizzled out because her one advantage over Judai would be out of her reach. Therefore, it is technically his friends' fault for getting themselves killed, not Judai.
The dub practically confirms this.
Kaiba founded Duel Academia to make up for how uselessly antiheroic he was during the original Yu-Gi-Oh.
We know Duel Academia was founded by Kaiba. It is later revealed that its purpose is to attract the superpowerful cosmic whosawhatsits and train kids to beat them. Kaiba was rather... against the idea of the paranormal back in the day, and thus was more often than not an obstacle to getting the world saved. Between the two series, he realized how much danger he put the world in due to his pride and made a place to do the world-saving in the foreseeable future to make up for it.
Kaiba didn't make Duel Academy to repent, but to continue his rivalry with Yugi; it's a giant attempt at one-upping Yugi's heroism via saving the world through his students.
Proof of this is shown in the way the dorms are listed. Obelisk Blue (Obelisk being Kaiba's personal God Card) is on top, and Slifer Red (Slifer being the first God Card Yugi got a hold of) is only for "slackers".
Yubel was male in his life as a human, but was castrated upon being turned into his current form.
He was young enough before the surgery to be androgynous, so no one knows for sure what his real gender was. Since the purpose of his transformation was to protect past-life Juudai until he reached adulthood, this would probably have been done as a measure to prevent him from becoming distracted from his duty. Also, Yubel has two voices, the voice it had as a human and a deep male voice which is never explained. If this is true, the male voice would be the voice Yubel would have had as an adult if he had stayed human, possibly indicating that he feels some regret for being turned into...whatever that thing is.
Season 4 didn't happen because Judai's fusion with Yubel lead directly and immediately into the events surrounding Zero Reverse.
The garbage surrounding the ancient history of the Jibakushin and the Nazca Lines are all blatant lies, and the Jibakushin have only existed for as long as Yubel and Judai have been fused. Furthermore, Rudger's destruction of Old Momentum which caused the Zero Reverse was a desperation bid to prevent Instrumentality - had Yubel and Judai not become fused, Zero Reverse would have turned into a black hole that ended all life in this and every other reality, and without Zero Reverse happening, everyone would have become tang. The two events canceled each other out, containing the catastrophe to a manageable area and leading directly into the Oddly Named Sequel, 5Ds.
The show is the result of a dimensional warping caused by Anubis.
Remember Yu-Gi-Oh the abridged movie? How Anubis showed the characters the grim future? Anubis actually caused this horrible fate by warping reality.
The plot of GX will be resolved in 5Ds
Similarly to how Judai went back to duel Yugi, Yusei will go back to duel Judai, but Yusei will stay and fix some things.
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