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Writer-Induced Fanon

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Let's say that a show strongly hints at the possibility of Susie having lost a baby as a teenager. Almost all of the fans accept this, but the hints are vague enough so that they can also be interpreted to support the idea that the baby that died was Susie's younger sister. Confirmation for the supporters of the first theory would come in the form of Susie over-empathizing with a mother who has just lost her baby and being very tight-lipped when Joe asks her why (why would be tight lipped if it was her sister?) and getting teary-eyed when watching mothers interact with their children. So while Susie losing her sister fits with the hints (though not as well as the more widely accepted story), it doesn't explain either of these situations, where Susie losing her daughter does.
Of course, there are alternate explanations for both of these situations, but really only one that explains them both, and the show has already hinted at it repeatedly. This is where writers want to include an idea — any element contributing to the plot or a character — in canonicity, but don't want to explicitly state it. As a work-around, the writers hint at the idea until it's accepted by most of the fandom. These hints are usually strong enough that most of the fandom gets the right idea fairly quickly, but not so strong that they can't be ignored or attributed to something else if the viewer dislikes the idea being hinted at. The point is, after all, getting the idea across to a large portion of the fandom while offering a less convenient, but still plausible, alternative explanation for those viewers who don't want to believe.
This tactic is most often employed when writers want to include an element such as mental illness, rape, homosexuality in older shows, or another sensitive topic in a plotline or a character's backstory as a means of plot or character development, but don't want to explicitly state it to avoid controversy or alienating certain viewers, and also to subvert censorship. The artistic reasons for doing this is Show, Don't Tell, it's more interesting to tempt readers to figure this out for themselves than explicitly spell it out. Likewise, the information in question is merely backstory and subtext to the plot in question. If a plot is an adventure/crime/heist/romance story, potentially disturbing and traumatic details might overpower the drama of the genre setting, so for a writer, it's better to put this in the background and leave it for the specially involved reader and viewer.
If the hints are particularly weak or ambiguous, it can be difficult to determine if they are deliberate or merely a coincidence. Short of a Word of God confirmation of intent, the easiest way to establish this is if the idea is built on as if it was canonical. Bear in mind also that, for this trope to apply, the fanon has to result from the hints. If the fanon existed with more than a few supporters before the idea was hinted at it's just fanon.
This trope is most common in live TV shows, but shows up in other mediums fairly often as well.
For when this happens with a ship, see Ship Tease. Can result from intentional Canon Fodder. Contrast with Wild Mass Guessing and also Applicability where a given work is deliberately written so as to be open to multiple interpretations rather than a single one.
 Writer-Induced Fanon
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Ben-Hur (1959) had a famous example in the case of the Ben-Hur and Messala rivalry. Gore Vidal admitted that he and William Wyler when considering what backstory to provide that might justify Messala's sudden and inexplicable betrayal of Ben-Hur settled on the idea that the two were male lovers in their youth but drifted apart and Messala persecuted Ben-Hur because he believes he has been rebuffed. Wyler instructed Vidal to tell actor Stephen Boyd but not Charlton Heston, which is why much later Heston innocently denied this claim and tried to downplay Vidal's contribution to the film.
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The Never Ending Story was basically written with the idea that its readers would write their own stories.
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The Haunting (1963) has Theo acting incredibly affectionate towards Eleanor and she behaves as if she were a love interest. Eleanor's line to Theo about "nature's mistakes" adds homoerotic subtext. There was even a planned opening that would have Theo in her apartment finding "I hate you" written on her mirror in lipstick - implying she had just split up with a female lover. Among fans it's universally agreed that Theo at least is gay. The 1999 remake made her an out and out bisexual.
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 The Haunting (1963)
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From Bones, Brennan having Asperger's Syndrome was an example of this until she was given a Word of God diagnosis. It's still an example of this if you don't consider the Word of God to be canonical.
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Community has dropped some heavy hints that Britta was molested as a child by a man in a dinosaur costume, with her online character bios outright confirming it.
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Hard Candy:
It's assumed by a lot of viewers that Hayley had been molested at some point. Her actual motivation for targeting Jeff and his accomplice Aaron is never stated but Elliot Page himself believes this to be the case - and played some of his lines with a kind of righteous bitterness, as if coming from a former victim.
A lot of viewers take a line from Hayley that was cut from the film - coupling with Elliot Page's Dawson Casting - that she's Older Than They Look and only posing as a fourteen-year-old.
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In Supernatural, the reason for Bela Talbot's Deal with the Devil to kill her parents being because her father molested her and her mother didn't intervene. There's also the pretty widespread theory floating around that Bela was the "weeping bitch" Alastair mentioned in "On the Head of a Pin" as the first soul Dean tortured in Hell and thus the first seal broken to free Lucifer.
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Renee Walker having been raped on 24. While it was pretty evident that she was raped by Vladimir Laitanan during the events of Day 8, the writers never more than hinted at the idea that she was also raped when she was undercover with the Russians before. This is one of the most widely accepted pieces of fanon in the 24 fandom, many fans even considering it canonical. This idea is later used to help validate what Renee ends up doing to Laitanan.
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In The Order of the Stick, Belkar Bitterleaf's asked if he caused the death of Roy, Miko, Miko's stupid horse, or the oracle, and got a "yes" answer. When Roy fell several hundred feet onto the ground to his death, many fans assumed this fulfilled the requirements, because without Belkar, Roy would not have been able to engage Xykon for that particular fight and thus would not have died. Later it turned out that the prophecy was less ambiguous as when told this by the Oracle, Belkar doesn't buy it and promptly stabs him to death. The reason why it's here is because in the compilation comic, Rich Burlew says he deliberately set this trope up so he could subvert it.
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John Dies at the End heavily implies that Dave was raped as a kid, but he refuses to talk about it. All he's willing to disclose is that he was held down by a group of bullies who did something awful to him.
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Pokémon Adventures: The Striaton Trio really being the mysterious Shadow Triad of Team Plasma, due to the overwhelming hints. The fact that it's a common theory for the games and anime helps. And despite all those hints, this theory is eventually jossed with the Striaton Trio battling the Triad.
For an example dating back all the way to the first generation, it was assumed for years by fans that Mr. Fuji, of Lavender Town, was the scientist who created Mewtwo in the games, who then retired to the Pokémon Tower to repent. Though Mewtwo's creator in the movie is called Dr. Fuji, he looks nothing like his game counterpart and their personalities are very different — however, this is par for the course for the early anime, so it deterred no one from thinking that it is true in game canonicity as well as anime canonicity. Despite one line of dialogue that might possibly suggest that Game!Fuji was at Cinnabar Island at the time that Mewtwo was clonednote though all it says is that he is friends with Blaine, and few people would have read it before the remakes came out there was still no clear evidence that Mr. Fuji even knows of Mewtwo's existence. However, the Pokémon Origins special does have him be the only person in Kanto who knows about Mewtwo, but still does not go out and say that he in particular cloned him. Most fans have taken it as confirmation, though.
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 Pokémon Adventures (Manga)
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It is hinted several times in Slayers that Naga is Amelia's older sister.
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In Avatar: The Last Airbender, Zuko's mother was banished for committing "treasonous acts", however it's never stated what these acts were. Coincidentally, she was banished right around the time Fire Lord Azulon died. It was widely believed amongst the fanbase that she was responsible for his death until it was finally confirmed to be the case in Season 3 (although it was done at the behest of Azulon's son (and her husband) Ozai, who threatened to murder their son Zuko if she didn't comply).
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At no point is it ever actually stated that Haruhi Suzumiya is set in the author's hometown of Nishinomiya. It is just very strongly implied, thanks to the animators going out of their way to faithfully replicate real locations in the area.
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Touken Ranbu: Cards number 1 and 2 will be D�jigiri Yasutsuna. This sword is one of the prestigious Five Great Swords and has been hyped up in-game long before any possibility of being confirmed as a character, and the very first sword in the character index, Mikazuki Munechika, is cards number 3 and 4.
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 Touken Ranbu (Video Game)
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For an example dating back all the way to the first generation, it was assumed for years by fans that Mr. Fuji, of Lavender Town, was the scientist who created Mewtwo in the games, who then retired to the Pokémon Tower to repent. Though Mewtwo's creator in the movie is called Dr. Fuji, he looks nothing like his game counterpart and their personalities are very different — however, this is par for the course for the early anime, so it deterred no one from thinking that it is true in game canonicity as well as anime canonicity. Despite one line of dialogue that might possibly suggest that Game!Fuji was at Cinnabar Island at the time that Mewtwo was clonednote though all it says is that he is friends with Blaine, and few people would have read it before the remakes came out there was still no clear evidence that Mr. Fuji even knows of Mewtwo's existence. However, the Pokémon Origins special does have him be the only person in Kanto who knows about Mewtwo, but still does not go out and say that he in particular cloned him. Most fans have taken it as confirmation, though.
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 Pokémon: The First Movie
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Likewise in Final Fantasy VI, it's never outright stated that Shadow is Relm's father, but it's implied strongly enough that it's regarded as canonical.
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Taxi Driver has Travis Bickle as a Vietnam War veteran. In the film this is casually hinted and not specified. Martin Scorsese and Paul Schrader discuss the subtext as if it had always been part of the film.
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From NCIS, Ziva having been raped in Somalia. It was hinted at by Gibbs and Vance throughout the beginning of the seventh season and is widely accepted fanon. The idea is further used throughout the seventh and eighth seasons to help develop Ziva as a character, as well as her relationships with other characters, most substantially Gibbs, Tony, and her father, but remains non-canonical.
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 NCIS
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Red vs. Blue:
Project Freelancer was probably a project competing with the SPARTAN program, based on Washington's remarks that "there were dozens of projects all trying to come up with the magic bullet to win" during the war with the aliens, Burnie saying Dr. Church used to work with Dr. Halsey (who was behind the SPARTAN program), and so on, but Spartans are never actually mentioned in-series, aside from semi-canonical references to Master Chief in the first episode and some of the PSAs.
On a similar note, the aliens are pretty strongly hinted to be the Covenant, with their worship of ancient technology, the war with the UNSC ending around the time of the switch to Halo 3 machinima, etc. But they're only ever called "the aliens" in the show (except, again, in the first episode and some PSAs).
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Tangled: The Series: Cassandra, Rapunzel's Lady-In-Waiting, is gay. This is pretty universally-accepted by the fandom, to the point where fanfic writers feel uncomfortable with the idea of writing her as not being gay out of a fear of invoking Hide Your Gays. The one time she seemed to have a male love interest, it turned out to just be a case of Keeping the Enemy Close, and she actually had no interest in him whatsoever. Given this, she could still be read as asexual, but her voice actress has stated that both she and the animators (many of them queer themselves) deliberately played her as gay as possible. Similarly, Rapunzel and the Lost Lagoon portrays her as Raps' Not Love Interest.
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Rebel Without a Cause by Nicholas Ray has Sal Mineo's character Plato harbour a visibly obvious crush on James Dean's Jim Stark. The film's bisexual love triangle had long been considered canonical before it was outright admitted by Nick Ray in a TV interview, where he admitted that he, James Dean and Sal Mineo (who was himself bisexual) established the subtext and joked about how "this is for the movie buffs in France".
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Hetalia: Axis Powers: Himaruya has flirted with the idea that Germany is Holy Roman Empire with memory loss for a long time, but he has yet to confirm it.
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Considering ZUN's tendency to keep things vague and leave things implied in order to allow for fan interpretation, it should come as no surprise that this is pretty common in Touhou Project:
While the exact nature of the relationship between Maribel Hearn and Yukari Yakumo isn't clear, ZUN's mention of Lafcadio HearnNoteLafcadio Hearn was a European writer who changed his name to Koizumi Yakumo when he became a Japanese citizen when asked about it has led many fans to assume that Yukari is Maribel's future self, and that the latter will at some point become Trapped in the Past and have to take The Slow Path.
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Fans of Psychonauts have come to the conclusion that psychic kids tend to mature much faster than non-psychics. The kids at Whispering Rock Psychic Summer Camp range from ages 7-13, but they act like they are much older, with an ever-shifting web of romantic couples. Their unusually mature personalities might simply be due to Most Writers Being Adults, but there is a lot of evidence to support this idea.
It's heavily implied that there's a lot of prejudice against psychics in the rest of the world, and most of the kids have severe mental issues.
In one of Sasha Nein's memory vaults, we see that he was traumatized as a child when he read his father's mind in order to see his dead mother and accidentally saw her naked, and we know that Elka, one of the campers, foresaw one of her parents' having an affair.
Plenty of the kids are also telepathic and are likely to have heard things that no one would ever say aloud around a child.
All of this together suggests that most psychic kids have to deal with a lot of heavy, traumatizing stuff even at a young age, forcing them to grow up quickly.
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The Teen Titans fanfic New Tamaran shares an awful lot of story details with rumors about the show's unproduced sixth season. These include:
Being focused on Starfire.
Blackfire as the main villain.
An alien invasion.
Terra and Slade both return.note But only as cameos.
Robin becomes Nightwing, and Raven becomes White Raven.
Being Darker and Edgier than the show.
Bringing back Season 5 Titans.
Beast Boy and Raven become a couple.
Robin and Starfire further their romance.
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Twisted Wonderland: Dire Crowley is a fairy. It's never canonically made clear what species and how old he is, but he has pointed ears, which is a trait otherwise only seen in fairies.
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Blade Runner has the famous "Deckard is Replicant" issue. Ridley Scott is quite keen on the idea that Deckard is a Replicant over the objections of the screenwriters and Harrison Ford himself. Scott got the idea mid-production. It wasn't originally in the Philip K. Dick novel note  while Deckard in the novel is at one point accused of being an Android, it's quickly revealed to be an attempt at gaslighting him, and a self-administered empathy test proves that he's human. , nor was it planned at pre-production. Harrison Ford feels that Deckard has to be the main human being the audiences can relate to and properly be an Audience Surrogate and he was openly angry when Scott tried to insert the Unicorn origami scene since he caught on what he was trying to do. Hampton Fancher in any case feels that Deckard's humanity or lack thereof should never be openly addressed and become part of the surface experience of the film, and remain an issue of speculation.
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Final Fantasy
Though it is never explicitly spelled out, the clues add up enough so well that fans of Final Fantasy VIII universally accept the idea that Laguna is The Hero Squall's father.
Likewise in Final Fantasy VI, it's never outright stated that Shadow is Relm's father, but it's implied strongly enough that it's regarded as canonical.
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The Doctor's Mysterious Past has had messy implications heaped on it by every passing writer for the past half-century:
The First Doctor is implied to be an outlaw, exiled from his home planet and forbidden from returning. Later fans and writers have run with the implication, as well as some Early-Installment Weirdness, to suggest his fear of interfering with past events (or, from a Doylist perspective, the fact that purely historical adventures were most common in his era) is to avoid catching the attention of the Time Lords, and that he left Susan on Earth in 2164 so that she wouldn't be caught by them as well.
The outlaw characterization is played up with the Second Doctor, who further implies he's the only survivor of his family. The Doctor's race is finally named for the first time, but their punishment of him complicates the circumstances under which he left his home world in the first place, raising the question of whether he's cast out from his people or if he escaped. In his final story, we meet his people in the form of both the Time Lords in general, as well as a particular one titled (but never named) as "The War Chief", who wears a dark jacket, a Dastardly Whiplash goatee, and who's using mind control powers to try and take over the galaxy.
The First and Second Doctors' eras together primarily imply the Doctor is fundamentally human (including a single heart), but has been changed by his time travel; this gets overwritten by the reveals of the Time Lords and the Doctor's alien anatomy.
The Third Doctor's more aristocratic bearing was retroactively applied to the character, playing up the idea of him having been a "Lord of Time" more seriously than the first two Doctors really ever seemed to. The Third Doctor tells stories of having been an aimless, unhappy aristocratic child on a boring, yet beautiful world. We're introduced to the Master, a fellow Time Lord who wears a dark jacket, a Dastardly Whiplash goatee, and who's using mind control powers to try and take over the galaxy, whose relationship to the War Chief is never made clear in the actual program. He also tells stories of a mentor who helped him who is strongly implied to be the Time Lord that eventually helps him to regenerate into...
The Fourth Doctor's immediate and urgent abandonment of Earth in general and UNIT in particular was likewise projected onto the past incarnations of the character, reframing his escape from Gallifrey as having been not because of some obscure but terrible crime or the death of his family, but more because he just couldn't sit still for one more second when he had the option to travel all of time and space. Even when given the opportunity to rule Gallifrey and "fix it" as he sought fit, he eagerly left it behind. Around this time, the concept of "Renegades" became somewhat more solid: The Doctor and the Master were so called because their actual names are, to some degree left to Fanon to clarify, unspeakable. The Fourth Doctor also was seemingly intended by long time writer Robert Holmes to be the final (or, at least, penultimate) Doctor, when it was revealed that Time Lords only have 12 regenerations, and a story seemed to imply the Doctor had held at least 8 different faces before the televised first Doctor.
The Fifth Doctor's era brought with it a change in how his relationship with the Master was viewed. The idea of the Master as a supervillainous arch-nemesis had been clear since the beginning, but a long run of Master-centric stories in the Fifth Doctor's run shifted it to more of the Master being a Doctor-obsessed troll.
The Sixth Doctor's era cast the Doctor's wildly-inconsistent personalities into new light by revealing a possible future incarnation, a rules-obsessed Lawful Evil lackey of Gallifrey known as the Valeyard (which Fanon has interpreted to mean "a Doctor of Law"). The exact nature of the Valeyard is so ambiguous, though, that every sinister turn the Doctor has taken since then has been identified as the Valeyard (Grandfather Paradox, the Meta-Crisis Tenth Doctor, the Flesh Ganger Doctor, even the War Doctor when he was first introduced as a cliffhanger), a title it was confirmed in the Eleventh Doctor's era the Doctor will yet someday bear.
The Seventh Doctor brought with him the Cartmel Masterplan, an attempt to infuse the character with more mystery and power after decades of Gallifrey stories had robbed him of his uniqueness. The implications the show played with were stark, casting the Doctor as a Physical God of Gallifrey who stepped down and fled in a past far more distant than had been implied before. The further implications were made clear in the Expanded Universe, where the Doctor was revealed to maybe be the re-incarnation of the Other, one of the holy trinity of the Time Lords (the other two being Rassilon and Omega, the Big Good and Big Bad of earlier episodes), but the books are of ambiguous canonicity.
The Eighth Doctor's somewhat absent era makes it rife for fandom interpretation. When the series returned with the Ninth Doctor, the implication was that the horrors of the Time War had been experienced by the Eighth Doctor, a somewhat inoffensive and charming character for whom it would all be terribly crushing to have to experience. Conveniently, the books had been wrapped up in an incredibly dense and yet incredibly unclear narrative about a war in time that destroyed Gallifrey for years by that point, so Fandom set about merging the two concepts in various ways. The Eighth Doctor was also the Doctor that infamously declared himself half-human, but in circumstances where he could be either joking or lying, with the Master's assessment of his retinal structure suggesting he wasn't.
The Ninth Doctor's era introduced the Time War to the series, creating a new justification for why he was the most important and unique of all Time Lords (namely, the rest were all dead). It also seemed to imply that the first ever companion, the Doctor's granddaughter Susan, was dead as well. Other mysteries lurk in the Ninth Doctor's era, mostly revolving around how fresh his face was in his first episode and whether he knew or had anything to do with Jack Harkness's past life. The big mystery, though, is whether the Ninth Doctor A: is canonically Bisexual, and/or B: is the first Bisexual Doctor.
In the Tenth Doctor's era, the show again flirted with the implications of the Other, with characters noting that the Doctor was something strange, mythic, and terrifying even by Time Lord standards. The Tenth Doctor's era also introduced the aforementioned Meta-Crisis Doctor, who (due to retcons) ended up being numerically correct for the Valeyard's "between your twelfth and final incarnations" placement and was born of blood and battle and fury, and who would age and be unable to regenerate, all of which lead to some very common fanon regarding his fate. This was also the era where the running title gag of "Doctor Who?" started to gain more significance, with Madame de Pompadour declaring it "More than just a secret". Elsewhere, the era raised questions of what the Doctor's relationships with his companions really are, and really have been. The finale also featured a mysterious character who Fanon has made numerous vocal identifications of, the loudest being that she's the Doctor's long lost mother.
The Eleventh Doctor's era recast the entire name issue as being tied up in a prophecy regarding the most mythic event in the new series: the Time War (though numerous Red Herring reveals along the way confused matters). Also, as the series went on, a great number of plot threads were Left Hanging due to time or casting constraints, leaving much of River Song's biography and the overarching Myth Arc ambiguous and up to Fanon to clarify.
The Twelfth Doctor's era very strongly implied romantic feelings between him and Clara, his primary companion. It also implied the First Doctor's gender identity might not have been as fixed as it seemed.
The Thirteenth Doctor's era took previous hints about the Doctor having had lives before the First Doctor, and about them having been present for the origin of the Time Lords, and made them explicit fact, creating a new story around them: the Doctor's full past had been hidden from them by having them subjected to Laser-Guided Amnesia and regenerated into the child who'd become the First Doctor. In truth, they were the "Timeless Child", an extradimensional being of unknown origin with the capacity for infinite regeneration, who'd been discovered by the first Gallifreyan space explorer and used as the basis to give the early Gallifreyans their own regenerative capabilities, and among their forgotten incarnations were the 8 mystery faces from the Fourth Doctor's era. Though the Other wasn't explicitly mentioned in this, there was space where an early incarnation could have taken the role.
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In Power Rangers RPM, various characters show signs of arrested emotional development: Dr. K has No Social Skills, and Sixth Rangers Gem and Gemma have all the emotional maturity of five-year-olds. All three were Child Prodigies that were abducted from their homes and denied normal childhoods, spending most of their lives in a military think tank called Alphabet Soup, so most fans blame that for inflicting emotional abuse on them.
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In Harvest Town, many fans pretty much take it for granted that Julia Allen is having an affair with Steve Lopez after a Quest reveals a picture of Steve with a woman that looks suspiciously like Julia. The possibility that the two might have dated before Julia's marriage to Peter Allen (as Julia is said to have been a beautiful woman with many suitors) is rarely considered.
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Though it is never explicitly spelled out, the clues add up enough so well that fans of Final Fantasy VIII universally accept the idea that Laguna is The Hero Squall's father.
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 Final Fantasy VIII (Video Game)
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Someone on the fan list for Adventures of the Galaxy Rangers (where several of the show's writers lurk) brought up the disturbing possibility that the Queen didn't put Zachary in the Psychocrypt right after his capture, but decided to take out some frustrations on him first, especially since the scene where she's standing over his unconscious body was dripping with some disturbing implications. One of the writers delurked to admit that the writers themselves had very off-color speculations about Her Majesty's sex life. It's about a 50-50 split in the fandom whether she "just" used Mind Rape, or went for something more... inappropriate for an animated show.
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Gravity Falls and Rick and Morty are made by different companies for different demographics, but both have characters (Ford and Rick) who travel between dimensions, with implications that they've been to the same dimensions and/or met. (For example...) GF creator Alex Hirsch has implied that these references were meant more as jokes, but you can find plenty of fanart and fanfics that take the concept seriously.
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