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This is a "Wild Mass Guess" entry, where we pull out all the sanity stops on theorizing. The regular entry on this topic is elsewhere. Please see this programme note.
X-Men
aka: X-Men
Jack Winters (the Living Diamond), is Emma Frost's father

Jack Winters the Living Diamond from X-Men #40, was an evil mutant with telepathic powers who, as a result of exposure to a radioactive element, mutated even further into a man made of "living, flexible diamond." This power combination, telepathy, combined with the ability to turn to diamond acquired as a further mutation later in life, is incredibly idiosyncratic. What we saw of Jack showed him as a working-class, criminal sort, bank robber and burglar, which fits with Emma Frost's background as growing up poor and working class. Jack Winters was certainly old enough to be Emma's father, as a balding male when Cyclops was barely post-pubescent (and it is known Emma Frost is the same age as the original five X-Men). The two have oddly similar last names: Jack Winters, Emma Frost.
  • We do get to know Mr Frost, but given how screwed up their family was, assuming Jack Diamond was secretly Emma's natural father doesn't seem so far fetched.
  • But how would Cyclops respond if he found out this was the case? I mean finding out your ex-girlfriend is the daughter of your abusive foster father who you were forced to kill by your next foster father is pretty soul destroying. Although given how their relationship started par the course with his relationship with Emma.

One of Sunfire's mutant powers is longevity.

Sunfire's parents were killed by America's use of atomic bombs on Japan. Assuming he was a baby, that would make him about 67 in 2011, and thus far there hasn't been any explanation of his longevity. Baron Zemo II has a similar origin, although his longevity is explained by regular use of Chemical X.

It's possible the atomic bomb reference may be "topical," but 1) thus far all World War II references haven't been topical (with the possible exception of Ben and Reed's wartime careers), and 2) it's something of a defining moment for the character difficult to shift off to a later event like Tony Stark's Vietnam origin.

Wolverine's healing factor requires periodic use of his claws
Wolverine's old, uses his claws a lot and doesn't age. Meanwhile Old Man Logan has him being old and not using his claws since the villains took over and aging. Clearly he needs to use his claws to keep his healing factor sharp.
  • Doesn't merely having adamantium bones in the first place keep it busy?

Apocalypse isn't immortal, just hiding his age with the rejuvenation chambers.
I find it hard to believe that someone could simply be born immortal, so he's about 85 but the chambers keep him young and fresh.

Alternatively, Apocalypse has Healing Factor related Longevity.

Destiny was infertile
In-universe explanation for why Mystique was originally going to be Nightcrawler's biological father, but was later decided to having Azazel be his father. Mystique's original plan was to get Destiny pregnant as a man, but when Destiny was tested for infertility Mystique sought an alternative solution. Azazel was understandably surprised, but agreed to the deal. 9 months later, Kurt was born.

The current Bishop is not the same as the 90s character.
Given the massive Character Derailment, and the fact that his home future that's been seen recently bears only a passing resemblance to the one described in 90s flashbacks, he's obviously been switched with an Alternate Self.

Wolverine is Jesus in disguise.
That whole thing about being a Canadian from the 1700s? Total Red Herring and he's really a poor carpenter from Israel who was born around 1 BC. Think about it both were short and Jesus was presumably hairy. Wolverine could survive crucifixion and come back a bit later after being knocked out. Also Mary Magdalene is often associated with red and to quote wolvie in that awful new Spider-man cartoon he "likes [him] a redhead." Also something about Dan Brown. As for the complete change in personality? Well thinking about all the terrible stuff that the universe has put wolverine through in the last 200 years alone I wouldn't blame anyone for being a dick if they went through that kind of crap for ten times longer. As for how he is on so many teams at once? Jesus did it.

Xorn was Onslaught.
After the events of Onslaught: Marvel Universe he survived as a ghost on astral plane, Shadow King-style. After mustering up enough strength he possessed Xorn and created the solid telekinetic projection of Magneto's face containing his white hole of a head. And later he inhaled the drug containing alien parasite Sublime who started to fight Onslaught for control over Xorn's body which explains the subsequent irrational behavior of "Magneto". All that and the murders they had forced Xorn to commit drove him insane so when he came back in New Avengers he was a genuine sociopath.

The entire Mutants as Metaphor gimmick is a well placed Batman Gambit to make the fans really think deeply about them.
I realized this a while ago when posting on the JBM/Headscratcher page. Some fans Agree that mutants are dangerous and a Mutant Registration act is actually a plausible idea. Think about it, this is the exact thing Marvel wanted to do with Civil War. Look at it carefully:
  • For Mutants are Dangerous:
    • Omega Level mutants can kill entire worlds and in some cases have done.
    • Mutants can be unstable and Ax-Crazy psychos with Destructive powers is hardly unheard of.
    • They do pose a real threat.
  • For Mutants are people too:
    • Omega level mutants are rare and Non mutant-Supers are just as dangerous, if not more so.
    • Everyone can be unstable, including non-mutant supers.
    • The Majority of mutants before House of M are harmless.
So The writers had really planned for the readers to notice both these points, so they can really have a 'Which side are you on?' gimmick.

Klaus Schmidt is a cousin or brother of Johann Scmidt.
Now, I realize that the surname is merely the German version of "Smith," but it is remarkable how similarly they both turned their back on National Socialism as an economic policy in of itself to embrace even worse evil, if you consider it.

Deadpool really is a mutant

While he was artificially endowed with his healing, he already had one mutant ability shared with Squirrel Girl and She-Hulk: The ability to see the Fourth Wall. However, he is officially classified as a mutate, due to behind artificially endowed with another power, so when characters insist he's not a mutant, they're technically right as a mutant in Marvel's sense means to only have powers they were born with. However, it means mutants like Beast, who's powers were artificially upped and as such no longer fitting the classification, actually have no right to tell him he's not allowed into the X-Men on the grounds of not fitting the classification of mutant. So he is a mutant, but not anymore.

Dr. Manhattan created the X-Men
Bald guy with freaky abilities? Check. Most popular character is a mass murderer? Check. Is it a Mind Screw? CHECK!
  • X-Men created before Watchmen? Check. X-Men and Watchmen coming from different, competing companies? Check.
  • Doctor Manhattan being an omnipotent being who is dislocated from time? Check.

ALL Mutants have the power to come back from the dead.
It would explain so much.
  • It doesn't explain Doug Ramsey. Or Laurie Collins.
    • Wait for it...

  • Well just remember how long it too Siryn in X-Factor to accept her Father was dead. Her exact phrasing was somewhere along the lines of "Banshee is an X-man and they always come back." So perhaps the statement should be all mutants who are X-MEN (main team members to exclude X=Corp) have the power to come back from the dead...unless it's the future and Armor just snapped your neck or burned out your healing ability.
    • All mutants who are X-men, and Magneto!
      • And the Maurauders, and Madelyne Pryor, and Omega Red, and Unus, and...

Everything shown in the X-Family-related media is a result of psychic manipulation.
Every use of mental powers that looks the slightest bit fishy is proof. Everything that might disprove it is a memory fabricated by psychic mutants to cover their tracks. First, Xavier led the hive mind; later, Emma Frost took over. In the Ultimate Marvel universe, they rule separate hives.
  • Except in the Ultimate universe, it's been pretty firmly established that Frost's only power is the "turn to diamond" trick. She's not a psychic.
    • Not quite, at least once telepathy was hinted. It is possible, she did hide them.

The Celestials who added the mutant "x-factor" gene to humanity feed on psionic energy released by mutant powers.
All the battles between mutants are hors d'oeuvres to them. The powers themselves are a side effect. The reason all mutants are different is that they like a variety of flavors.
  • ... And now a variation of this theory has been used in the new Eternals series, with the Deviants being the multiflavored snacks. Do the Knauf brothers read TV Tropes?

Alternatively, The Celestials created the mutants to sow the seeds of bloodshed, which they could use as human sacrifices to feed their Magitek industry.
In The Eternals, The Celestials' technology is described as being made of rock imbued with magical power. Various magical traditions believe stone can be enchanted by absorbing the blood or Life Energy of people sacrificed upon it. The Celestials plan to sit back and watch the superpowered freaks they created wipe out each other & the normal people; then, when there's nobody left, they will harvest the bedrock of the planet, which will be empowered with massive amounts of magic energy by the deaths of entire species, and use it to build countless devices for export throughout their intergalactic empire.
  • And Aaron Stack was sent away for getting too close to the truth.
    • Nah, he's just a total ***.

Corsair is just fine.
At the risk of being a Captain Obvious... it seems unlikely that Corsair's really dead, even though he's the sort of C-List Fodder that you can get away with killing. (He hadn't been seen for some time, and so he's more expendable to The Verse than characters who got a lot deader.) Anyway... "The Rise and Fall of the Shi'ar Empire" was a lot bloodier than many an X-Men arc, with limb-ripping ahoy. Corsair's "death" was much cleaner than any other in the entire arc (and there were many), and his body was buried on a habitable but uninhabited planet... the perfect place to leave a character you want to get better but not return right away.

The scene where Phoenix fights Galactus is from the future.
The Phoenix lander recently discovered water ice in the Martian arctic. This discovery leads to people building Martian colonies and surviving a catastrophe that destroys all humans on Earth. (Probably an asteroid impact or pollution) However, humanity survives, because of their Mars colonies, and in the far future, people only remember that "Once there was a Phoenix that dealt fierce blows to a destroyer of civilizations."

The Phoenix will Retcon out the Decimation, End of Grey's storyline, Civil War, and One More Day once Joe Quesada leaves Marvel.

Jean Grey's gonna come back. When she does, she'll find out the world's been rewritten since she's been gone into a place she really, really doesn't wanna be. So, either we have another cosmic temper-tantrum looming on the horizon, or one massive Fix Fic by the Powers that Be after Quesadilla leaves. Maybe both.
  • Or she will show it to be all an illusion by some mad god trying to alter reality. It doesn't make sense for all that to happen in the Marvel universe even in an erased reality, because that implies that the erased reality was still a possible reality. It should be revealed as something like Mojo rewriting the universe according to some bad fanfiction he wrote.
    • Or that it never happened at all, it was only someone's bad fanfiction (well, it is just that in reality, so why not in canon too?)
      • Orrrrr Jean Grey and the Phoenix get over their collective mental problems and realize something is fishy so she gathers a dream team of dead and forgotten characters to help her find, gang-up on and collectively beat the ever loving crap out of whoever is doing this. (the characters I have in my head for this are Wasp and the Pat Mulligan version of Toxin) Cue them finding Mephisto about to erase the Parker's marriage while hiding either a Cosmic cube or the Infinity Gauntlet behind his back. Cue the Phoenix smacking the Macguffin out of his hand and a hilariously over the top curbstomp battle. Then they could either just retcon stuff out at their leisure or they could pull a Crisis on Infinite earths style reboot.
      • Honestly, I would love to see Phoenix tapping Mephisto on the shoulder and his Oh Crap expression thereafter.

Apocalypse is a lost Primarch

Think about it: he's immortal, his parents are unknown, he was found in a place a baby shouldn't be able to survive, and he is trying to take over the world. The way he looks is a result of Warp mutation.

Mutants are actually several different subspecies.
Even if all mutations are activated by the same genetic sequence, mutants can pretty clearly be separated into elementals, psionics, superhumans, and bestials.
  • What about mutants with multiple powers or secondary powers that are different from the first? Emma Frost comes to mind. Are they hybrids?
    • One assumption would be to go by whatever is considered the primary power. Wolverine, for example, is known best for his metal claws and bones, whereas his healing factor is only ever mentioned if he gets hurt.
      • The metal isn't a power, it's an external effect that he survived because of his healing power. It's bone claws (bestial) or healing power (superhuman).
  • The implication is that all mutant powers are basically psionic; in one early story mutants with multiple unrelated powers, some of them seemingly physical, are used by the Secret Empire to power a superweapon (a lame unarmed flying saucer "superweapon", but still.)
  • They're really more like breeds. Somewhere, a taxonomist is crying.

Mutants all have one power: the first instance of major duress in their lives activates a corresponding power based on their personality and the problem at hand to protect them.

Most mutant powers seem to be random. The X-Gene is actually a complicated, semi-sentient genetic code that activates when its host first experiences stress and applies a reactionary solution to the problem.
  • Kitty Pryde's "reactionary solution" to being nervous about meeting her prospective new boarding school principal and having a killer migraine was to fall through the floor and land directly on her butt in front of her parents and said prospective new principal?
    • She was thinking of jumping through the wall and running away. It didn't work out quite like she planned.
  • Alex Summer's was activated to defend himself from the Living Pharaoh.
  • Angel's love of heights caused him to develop wings, not vice versa as it's implied.
  • So that means that Darwin is nervous about everything?
    • There was a story in a Hulk annual where Doctor Samson theorizes that getting powers from gamma rays is expressly tied into your personality and its desires.
  • I thought the idea of peoples' personalities unconsciously deciding their powers was somewhat canon? Or maybe I'm mixing it with fanon, since I've heard of this idea more than a few times over the years. Though in some instances it doesn't seem to make sense: Jean Grey's reaction upon seeing her friend die is suddenly reading everyone else's minds? Cyclops' reaction after losing his family and living in an orphanage is to shoot red beams out of his eyes? Storm makes sense, Colossus makes sense, but after a while, the theory kind of fails. Or maybe it's that only the stronger personalities can select their powers, whereas those who aren't as willful get whatever the gene gives them?
    • Same troper as above: then again, I've also heard of the environment deciding, usually in regards to Storm.
      • Cyclops' power just needs to be interpreted a little symbolically to make sense. So, we know he's this absolutely stoic, Sugar and Ice Personality who represses his emotions in order to deal with life. I think that his Eye Beams are the manifestation of all the emotion and trauma he bottles up in his soul. Note that the beams are impossible for him to control/stop, under natural circumstances (He needs to close his eyes to do so if no glasses are available, which in itself is very interesting symbolism.) They're also bright and heavily destructive when he does show them- not easily ignored, and Scott's angst over not being to turn them off divides him from others and cripples his emotional self-confidence. If we assume that his beams are the outer expression of Scott's hidden pain, given form by the X-Gene, a lot of things start making sense. (Although this almost certainly wasn't what the authors intended.)
      • Jean, we know, is the Team Mom, and very insightful as to how others are feeling/thinking- even without telepathy. But more than that, her telepathy is a gateway to the Phoenix Force, which allows her to channel godlike energy. Depending on the canon you follow, Jean always knew this subconsciously. Maybe Jean's desperation over her friend's death led her to reach for this power- power enough to, she hoped, save her friend. Either that, or this was Jean's telekinesis unlocking itself. Telekinesis would be very useful in trying to avert a car accident.

Magneto has been playing everyone, or really really fails.

He can generate magnetic fields of several million Gauss. Magnetism is, as we all know, an aspect of electro-weak force. He should be able to induce radiation and massive electrical fields at will. He should be able to throw ball lighting and kill with a thought.
  • Why should he do that when he can just magnetically rip out your blood using the traces of iron it contains?
    • He can do all that, but only when the writer remembers or has any knowledge of physics, or when it wouldn't make the story last five seconds because the entire X-team just got flash fried.
      • See the "mental blocks" WMG below.
      • Another common explanation is that feats like that take a lot more out of him than just controlling metal.

Wolverine is a Dungeons & Dragons troll with some make up slapped on
This explains the regeneration, plus every time Wolverine is cut up, a new Wolverine grows and joins a super hero team. This is how we have Wolverine Publicity, because he really is everywhere
  • ...this reminds me hilariously of an episode of the 90's X-Men cartoon, where Jubilee told some kids a campfire story where the Wolverine Expy was a troll.
    • Which was based on the comic, where Kitty is the one telling the story to a sick Illyana.

Alternatively, Wolverine has another mutant power: colocation.

That's why he can be having adventures with the X-Men, the Avengers, and on his own in three different parts of the world simultaneously. No one notices or thinks to call him on it because, compared to Wolverine's other powers, colocation is pretty subtle.

Layla Miller is the Marvel Universe's Haruhi Suzumiya, and X-Factor is her SOS Brigade.
It does make sense that a girl whose never appeared before House of M could have a massive ability to have an impact on reality due in part of Scarlet Witch. Her powers is to spot changes in reality, restore the memories of an individual in said altered reality, the ability to spot paths of causality and a chance to change the results, and precognition, but that could be her changing reality and changing it back every little while? She subconsciously rounded up a group of people to keep an eye on her after House of M and willed everything in the series to happen herself.

The Homo superior thing is not just Artistic License - Biology, but someone's propaganda

In mainstream Marvel continuity, the idea of mutants as a "new species" doesn't stand up to biological scrutiny [or even far less so than the idea of superpowers]. Mutants are described as being a single new species, but they're wildly divergent variations off a clear human mainstream. Mutants and humans can interbreed and produce viable offspring; more pointedly, humans can have mutant babies, and mutants have had normal human babies. Mutants aren't an isolated population speciating from normal humanity; they're a population distinguished from normal humanity based on strangeness.

People like Steve Rogers, Bruce Banner, and Peter Parker are considered "human" because their powers manifested after contact with radiation or drugs. Scott Summers, Jean Grey, and Erik Magnus Lehnsherr are not considered "human" because their powers didn't manifest after contact with serums or gamma rays. Yet, rising levels of ambient radiation due to nuclear testing have been cited a few times as a cause for the growth in the mutant population during the latter twentieth century.

Word of God at different times has suggested that the Celestials long ago put a "kink" into human DNA allowing the development of powers. Perhaps it's all part of the same biological mechanism, and the only real difference between a mutant and an "altered human" is how close somebody was to having that superhuman capability triggered (either through genetics, environment, or both) and therefore how little an impetus it took to push them over the threshold. (Consider how nobody's managed to properly duplicate the super-soldier serum's effects. Perhaps it's because nobody else had Steve Rogers.)

Going by the weirdly biased name Homo superior itself, which would more likely have been called Homo mutandis or some such by a reasonable biologist, the whole "mutant species" idea was probably coined by a mutant supremacist very early on. Human reactionaries seized on the fear of mutants supplanting humanity, and unfortunately, even peacefully-inclined mutant separatists like Charles Xavier found the idea useful or unavoidable.
  • The name, at least, comes from Magneto, who used it when taking over an army base in X-MEN #1. So yeah, propaganda.
    • Wait, so why does Prof X still use it? Is he just a dick?
    • Well, some versions like Ultimate Xavier did showed dickish behavior.
  • The name Homo Superior long predates the X-Men. It started in the 1930s, before Evolutionary Levels (and its dark side social Darwinism) were debunked.

Storm isn't really the happily married wife of Black Panther. She's acting as a secret agent.

That whole "Wakanda won't share the cure to cancer with the world cause y'all suck" thing? That really burned Storm up. So much so that she decided to infiltrate Wakanda, obtain the cure for cancer, and smuggle it back out. And what better cover could she have than the wife of the ruler of Wakanda? The divorce papers are already lined up, once she's got the secret, she's out of there!
  • I like how the fans have ideas that make more sense than the actual writers.
    • That's because we're actually trying to make sense of it, while the fanboys in charge are just doing whatever they think would be neat to try out that day.

The government is fanning anti-mutant hysteria... because they created them.
Mutants are the result of the government isolating the genetic quirk that gave Wolverine his fantastic and using it in a early version of the super-soldier program. The original test subjects displayed no superhuman abilities but it sure did pay of in the long term!
  • Except mutants were around long before the Government. The oldest one, Selene, has been around since the Hyperborean people.
    • Maybe she was created recently with false memories.
    • Also, Time Travel exists in the MU.
  • In Ultimate Marvel, so-called Mutants are the product of the Canadian (!) superhuman-project.

There is no Rule 34 in the X-Men universe.
And no Rule of First Adopters to help with mutant acceptance.
  • Actually, mutant porno has had a few explicit mentions.

Mystique and Changeling were/are the same person.
This is why the X-Men trust Mystique time and again despite her many Heel Face Turns—because Xavier trusts her. The Changeling never existed to begin with. He was just a cover identity. Any sightings of his ghost or his body being turned into a zuvembie are merely tricks of the imagination. Alternately, Mephisto did it.
  • Except that it's been established, thanks to alternate universes, such as Age of Apocalypse and Exiles, that Morph used to be Changeling when first starting out. In the Ao A, they're on two entirely different continents during consecutively running stories, X-Calibre and Astonishing X-men, respectively. Changeling died while posing as Professor X. The team keeps trusting her because she's just that manipulative, and the writers keep handing them the Idiot Ball.

Jubilee is actually the Jubilee line.
Well first, they share a name. Secondly, they're both new(ish). Thirdly, the resemblance between the London Underground logo and Jubilee's earrings in the '90s cartoon is uncanny.
  • So Jubilee's from London Below? Awesome.
  • I don't know why, but that idea makes me so happy after the whole M Day debacle. "Wondra." Argh.

Continuity Errors/Alternate Timelines/Comic Time/Multiple Wolverines are the result of the recent major reality warping events in the last couple decades.

Avengers Disassembled. House of M. One More Day.

All were major events that happened in a relatively short time apart in Comic Time. With the amount of stress placed on the 616 universe from all these events, something had to give. And something did. After surviving House of M's irreversible Mutant Decimation, the 616 Universe was permanently damaged, resulting in temporal anomalies. These anomalies include Compressed time (Comic Time), Spacial and Temporal Distortions (Having at least 3 damn Wolverines running around), and branching timelines that result in multiple pasts and futures. Every alternate continuity is a shock wave from the "ground zero" of 616's damaged existence with the epicenter being House of M, with One More Day and Avengers Disassembled amplifying the effects.

So yeah, thanks Spider-Man, Scarlet Witch, and pretty much mutants in general. No wonder you guys get so much hate, everyone throughout multiple timelines knows sub-consciously you're to blame for Crapsack Worlds like Days of Future's Past and Marvel: Ruins.

  • And then they all punched Superboy.
    • Don't forget all the weird stuff coming out of the cosmic events. The universe basically has had 2 major rips within a year from one another

The Quicksilver we see now is not the real Quicksilver, but a creation of Wanda's powers.

Wanda killed the real Pietro in yet another fit of insanity, and to deal with this, replaced him with one created from her reality-warping abilities, similar to how she made her children. At first, it acted much like the real Pietro did; however, as Wanda removed herself farther and farther from reality, so did the Pietro clone, and began to act erratically. When everyone realized Wanda was losing it, Pietro, being part of her mind and symbolizing all she wanted to hold on to, attempts to protect herself by urging her to create the House of M world. The reason why Wanda was able to 'resurrect' Pietro when Magneto killed him out of rage, was that it wasn't Pietro, but something she created from her memories. Afterward, without Wanda to direct his actions, Pietro went completely off the rails going off her last state of mind. It isn't until Wanda chooses to live in obscurity and relative normalcy that 'Pietro' begins to regain a modicum of sanity.

Magneto's powers actually make sense!
You see, Magneto has either reality warping, or energy control, just restricted by a mental block. He only can do things he thinks electromagnetism can do. This explains the Selective Magnetism. He's either deluded or misinformed.
  • Magneto having mental blocks about his powers has been implied in canon several times over the decades. It supposedly results from his realization that he could have saved his family from the Nazis had he known earlier that he had these powers.
  • Alternately, the mental block thing still applies, but his power is telekinesis.

Destiny was the Irene Adler.
...or at least was supposed to be when this would have only made her 90-something as opposed to 120-something. Think about it: who better to get the drop on Sherlock Holmes than someone who can see what he'll do?

Kitty Pryde will lead a revolt against Scott Summers' Utopia.
Once she recovers from having been stuck in the giant bullet, Kitty will take a good long look at Utopia and declare it a mutant ghetto. Given her ancestry (at least one grandparent survived the Holocaust), she's not going to like the idea of a mutant ghetto. And given that Scott left her to drift in the giant bullet, and Kurt died on Scott's watch, she's going to want to have words with Scott.
  • Didn't Wolverine also leave Kitty in the giant bullet? And since she and Wolverine have, traditionally, had a much much closer relationship than she and Scott, if she's gonna feel betrayed by anyone should it be him instead?
  • And Scott did try to get her out, in fact its said they tried all they could possibly do, they just couldn't. Utopia isn't a mutant Ghetto, really, its more along the same lines as the X-Mansion. Mutants live free of persecution, and train and learn to use their powers safely. The only problem they could have with it would be the same problems with the X-Mansion. Also, Kurt's death was a Heroic Sacrifice, and effectively saved all mutants. it wasn't either Scott's fault or anything he could have stopped or avoided. And as pointed out, Logan is just as much at fault, and with your logic, is just as much at fault for Kurt's death, probably more so since he was just with him.

There is another Sean Madrox.
Baby Sean Madrox received a slap while he was at the nursery. That made two of him. And one was kidnapped.
When we see him again, he will go by the code name of Chorus, having the powers of both his parents.

Wolverine is the Anthropomorphic Personification of gravity
Comics closely related to Wolverine (where he has a starring role) tend to end up revolving around him, as one mass does to the other, while comics that are only tangentially related to Wolverine still have him show up anyway, even if he doesn't do much - gravity has infinite range.

The Hulk's children shall become the new Horsemen of Apocalypse
And the Hulk will have to put aside his differences with Xavier and the X-men to take them down. Skaar will become the new War, Hiro-Kala shall become death, Carmilla Black will finally be confirmed as Banner's daughter and become the new Pestilence, and Lyra will become Famine because there was nothing left.

Mystique was Sherlock Holmes
...needs no further explanation.

Azazel was once a devout member of the Russian Orthodox Church
When his powers (and thus his demonic appearance) manifested, he was declared a demon, driven from his village, and excommunicated. The trauma of being exiled from his religious community is what drove him to embrace the atheism of Stalinism. Also, makes for very interesting contrast with his son.
  • I assume you mean Film!Azazel. In that case, it makes perfect sense.

Wolverine is an ephebophile
  • For a beer-swilling tough guy, Wolverine sure has a marked tendency towards teenage girl sidekicks, who tend to get replaced after the previous one gets too old. First was Kitty Pryde, age 13. Next was runaway orphan Jubilee, age unknown, but young. She managed to spend a while secretly living in the same Australian ghost town as the X-Men and stealing their food, apparently without Wolverine ever smelling her. Then came Pixie, age 14, and recently he was shown eating ice cream with new recruit Idie, age 14.

    Wolverine: No offense, but you trying to act... sexy... seems so wrong.
    Jubilee: Not thirteen anymore, Wolvie.
    Wolverine: I sort of wish you were.
    • Ultimate Wolverine certainly seemed to be. He slept with teenage Jean Grey, dated teenage Storm, secretly hid in bushes and watched teenage Scarlet Witch have sex with her brother, and tried to do something adult with Mary Jane Watson, high-school freshman.

    • And don't forget Hisako (aka Armor) in Astonishing X-Men.

Silver Fox is Rose from Origins
I have always believed that.

Nate and Hope are warring with each other for the fate of the world
But neither of them realises it.
When Nate re-manifested himself during Dark Reign, he had developed a few new applications of his powers, one of which was essentially precognition ('300 ways to tell the future'), which seemed to work by glancing at every way the future could potentially go from a situation and work out which were the most likely. While tangling with the Dark X-Men, he glimpsed the future that several have come to fear, where Hope wrecks the world and creates a dark and hopeless future. Essentially, what Bishop fears. He realises that in the future she uses her ability to mimic powers at their highest potential to copy his own unbelievably powerful abilities, and either tried abusing them or simply couldn't control them. Whatever she was trying to do to with them, it ends up with a horrific disaster that kills a million humans in an instant. Nate fears that any attempt to confront her directly would just give her the opportunity to access his powers, and uses the fight with the Dark X-Men to start an alternative plan. He somehow can't win a mental battle against Norman Osborne, he sets up the release of the Green Goblin persona which doesn't do anything to help him, and he walks right into a trap that gets his powers nullified. He then gets hooked up into the Omega Machine and is tortured by Sugar Man until he performs an action that burns out his power set...but not until the New Mutants arrive on the scene and are already battling to rescue him. The explanation for his powers being destroyed is acute nerve damage, which is an odd explanation for someone who has destroyed and reformed his entire body on a semi-regular basis. This was all part of a plan to only encounter Hope after he had lost his power set, denying her the ability to mimic it. Sealing his memory of what he foreseen was also part of his plan, trusting in himself to recover it as his powers returned and to find a way to stop the future cataclysm.
Unfortunately, what Nate didn't realise is that there's more to Hope's power than simple mimicry. It has been observed that people that she keeps close to her have a tendency to be affected by her, where they become almost respectful of her. Her Lights have been hinted to have fallen under her influence, and to not necessarily be wanting to stay with her of their own volition. Without his powers, Nate had no defense against this ability, and when Hope started working with him to train him in powerless fighting, he started falling under her influence as well, to the point where he has said he sees her as his sense of hope. She has noted that she thinks his powers are gradually getting stronger, and given her past of finding and igniting the powers of those who come to follow her, she may have the goal of helping X-Man get his powers back. By the time Nate recovers enough to remember what he saw, he may be too far under Hope's influence to stop it.
  • Hope's control is only over the Lights, which seems to be a by product of the Phoenix. People are only otherwise deferential to her because of what she represents. Also, this doesn't stand up, as Nate still possesses all the genetic potential for his incredibly vast powers. The only reason he can't access them is because his nerves are too fried after the whole thing with Sugar-Man and the Omega Machine. So if Hope was around him, she could theoretically access his godlike power levels.

Hope Summers is a Summers by birth
  • Thing the first: red hair and green eyes, while oddly common in the 616 Marvel Universe, isn't that common and only really comes with an X-Gene with one family.
    • Thing the Second: The part of the birth certificate that would allude to her father is blank, and her biological grandmother vaguely refers to her daughter having had several boyfriends. This means that her dad could be Cable, Stryfe or Nate Grey (all genetically the same person). There is some credence to the latter theory as while Nate was discorporated at the time, he discorporated himself a few months to a year before Hope was born and did the Mutant Messiah gig before Hope. Therefore, he could have psionically impregnated Hope's mother (work with me here, this is the X-Men we're talking about, and in particular, the dude who had a relationship with a woman who was genetically his mother - not that he knew that she was, of course). Or, since he said he was 'part of everyone', a slightly larger part of his essence could have altered Hope's genetics. And if it wasn't Nate, both Cable and Stryfe are time travellers, who both could have gone to impregnate Hope's mother as part of a stable time loop/Stryfe's latest attempt to screw with the Summers family.
    • Thing the Third: the Phoenix refers to her as 'my child'. Jean is the Phoenix. The Phoenix is Jean. The Phoenix has never been big on metaphors and cryptic - drama, yes. Cryptic, no. This means Hope is her daughter. Technically, she's either a clone a la Madelyn Pryor, or she's Cable's sister.

Kurt Wagner and Hank McCoy are both Muppets
Unless it's a case of interspecies adoption, The Muppets would seem to indicate than humanoid muppets can, like mutants, be born of human parents. And they certainly look the part. It might also explain why they're not bundles of massive angst.

Earth-616 Nightcrawler will come back to life.
Considering all the other major characters who have died and returned, it's no stretch. His teleportation ability will somehow factor in. When he returns he will have an awkward exchange with the Ao A Nightcrawler, who is currently in the Earth-616 universe.

Illyana is still dead.
In "Colossus: Bloodlines", we learned that Piotr Rasputin is a direct descendant of Grigor Rasputin, who needed a living descendant's body to inhabit. Unable to take over Piotr or his brother Mikael, he took over Illyana when he learned she was still alive. As the current Magik, Grigor coerced Colossus into becoming the new Juggernaut, and is now manipulating him to become Grigor's mindless slave.

Cyclops is currently mentally ill
A lot of people are quick to bash Scott because of the way he's acting is very extremist, or bash him for having an affair with Emma or whatever reason, but what a lot of people seem to forget is the reason why his affair with Emma started. Emma began giving him therapy because he was still suffering from PTSD and she used that to start the affair. Cyclops was unwell when it started, and instead of helping him she used it to have an affair. The entire thing meant that Cyke was in serious need of help, and by the end he lost his wife and was essentially mindraped by her from the future to push him past his guilt and have a serious relationship with her...But, he was never shown to be given any therapy for any of this or his already present problems. Then, there's what happened in Astonishing X-Men which likely screwed him up a bit, and the fact that students around him all lost their powers and got attacked and/or killed. Since that, The X-Men have been broken, pushed, and faced extinction, and during which Cyke never got any therapy for his numerous issues. The guy is a ticking time bomb waiting to break down, and that, combined with the situation, is making him behave how he is. Someone needs to do something quickly before he suffers a mental breakdown in the middle of a crisis.
  • There's also the interpretation that all the male members of the Summers clan have a genetic mental disorder, which would mean that Scott's would have been built on, if not by the brain damage, then certainly by the PTSD. Even if this was not the case then he still spent most of his childhood in the hands of either a madman or a criminal. So another question is why didn't anyone get him therapy as soon as he arrived in the school as a teenager, as it seems that one trauma after another has broken him down.

In the 90's cartoon, Cortez would escape the dimension as a more powerful mutant than ever before.
After being disillusioned by Magneto's unwillingness to attack humanity and Apocalypse using him, he starts to believe he himself is the true "messiah" of the mutants.

Somebody will try to make Dust wear more revealing clothes...and it'll go badly.
There've already been three alternate versions of her with a drastic change of character, and while this is my opinion I feel she's best the way she is (though granted the shyness part could use a bit more work in my opinion, but that's a different matter.)

Cyclops' new team will get their own book.
It will be titled something along the lines of the 'Unforgiven X-Men', and will feature X-Men and women who's credentials have been soiled by Never Live It Down moments and/or been considered villains at some point, as they try to keep peace between humans and mutants without support from others, save for SWORD. Like a mix between X-Force, X-Factor, and Xtreme X-Men. They won't be taking lives, but they'll be more proactive then previous versions of the group.
  • Confirmed, although it'll be the new Uncanny series (most likely for trademark reasons).

Chris Claremont created Excalibur to protect Kitty Pryde
Claremont could sense the rise of the Dark Age Of Comics and wanted to protect his creation, both from the overly-sexualized artwork of the future Image stars and from the likelihood of her being killed off as Marvel went Darker and Edgier. This way, he got to write her and Alan Davis, an artist with older sensibilities, got to draw her. Being able to keep Rachel Summers and Nightcrawler safe was an added bonus.

X-Men comics will have a lot of Sentinels in 2013/2014
Following Avengers VSX-Men, mutants are hated and feared more that ever before, which could cause the government to start using the Sentinels again. Also, considering that the Bad Future of the original Days of Future Past storyline was set in 2013, as well as the fact that the X-Men: Days of Future Past film is coming out in 2014, it will be a nice Shout-Out to the former and a great tie-in for the later.

Cyclops' current mental state is entirely caused by Emma Frost
Because in 90% of cases, being in a sexual relationship with your therapist makes your mental issues worse, this is the case even up to two years after the therapy. In Scott's case his therapist lied to him, telling him the only way for him to get better was to telepathically sleep with her, such a breach in trust would almost certainly place him in that 90%. Not to mention that none of his teammates seemed to care.

The Wolverine Publicity is a result of cloning.
He's already been cloned once, and suffers from amnesia. Who's to say that his regenerative factor, some scientists monkeying with his DNA or both resulted in Wolverine copies and thus he ended up everywhere. Hey, if Doctor Doom can make completely realistic and identical copies so that the fans don't say "they ruined Doctor Doom!", why can't James Howlett?

    Film series WMG 
Movie Cyclops is not dead.
How do we know Scott is "dead?" His glasses were floating. No body, no limbs, no blood. Nothing to show he was gone.

Jean just depowered him and wiped his memories. So, he ran off, leaving his glasses behind.

Xavier somehow knew this (maybe he read Jean's mind), so he didn't acknowledge the "death." Because she went ax-crazy and they had to deal with Magneto, he never got around to saying, "Hey, the Team Leader is not dead, but he has amnesia." So no one knew, and everyone thinks Cyke is dead.
  • Xavier says in the movie:
    "You killed the man you love because you couldn't control your power!"
    • Granted, Xavier could be lying to bring Jean out of her temper-tantrum.
    • Or she hid the truth about Cyclops from Xavier. She's more powerful than him. She could hide anything.
    • Xavier thought Cyclops was dead. See below.
  • It's possible that in X-Men 4, the X-Men will find him just waking up from a coma in a hospital in Alaska being treated by a doctor named 'Nathaniel Essex' (Mr. Sinister's alter ego), with his power temporarily turned off. Taking back leadership of the X-Men, he could show off his Badass Normal level of skill while displaying Astonishing X-Men's Cyclops-level of awesomeness, before regaining his power in a sudden surprise moment in the middle of a battle.
    • Or maybe they will find him years later, married to Madelyne Pryor, who is pregnant with a son.
  • In Superman Returns, there is a guy who looks just like Cyclops, just happens to be able to fly a plane with impossible skill, is at least as heroic as Superman since he's not invulnerable, and has a knack for hooking up with a woman who doesn't feel confident about their relationship. Clearly, Phoenix depowered Cyke and transported him to the DC Universe.

None of those who "died" by Phoenix Disintegration are actually dead.
They've been transported to another dimension. The Dark Dimension. Which tips its ruler Dormammu to Earth's existence. So the rebel Clea has to find a way to get to Earth and warn it against her Evil Overlord uncle. Oh, by the way, Xavier is comatose there. And Cyclops is sans glasses. Oh Crap. Well, there's other powerful mutants sent there by Phoenix.

The vestigial link between Xavier's unconscious body and the one he hijacked in Earth (just before being dispatched by Phoenix) will be exploited by Dormammu to invade Earth. And then shit will get real.

P.S.: Whether this will be a Doctor Strange movie or an X-Men movie is left as an exercise for the reader.

P.P.S.: Note to Hollywood writers: you are free to use the above idea in any way you like. I (JC Cy C) don't even want credit.

Sabretooth met Mr. Sinister between X-Men Origins: Wolverine and X-Men 1
At some point between the two films Victor Creed encounters Mr. Sinister, who enhances Sabretooth's mutant powers, but has the result of radically altering his appearance, making him much more bestial and animalistic.
  • It also gave him amnesia, which would explain why Sabretooth doesn't seem to recognize Logan.

Origins: Wolverine suffers from a case of Unreliable Narrator
It's still in continuity with the other films, as it's the story that Wolverine, perhaps after X2, has pieced together about his past, explaining both the plot holes and Fridge Logic. That's why it features elements that no longer fit, such as Xavier being able to walk, or some of the mutant cameos in the facility.

Movie!Psylocke isn't dead
She blended into the shadows as one of her powers dictates. Also as a Psylocke fan, I want her back.

X-Men 4 will be about Apocalypse
C'mon, how awesome will that be?
  • Hossed, X-Men 4 won't be about Apocalypse, but X-Men 6 is.

One of the mutants on Three Mile Island in X-Men Origins: Wolverine is Banshee.
Specifically the red-haired fellow with his mouth taped shut. You know it makes perfect sense.
  • And the one thrashing around trying to escape is Cannonball. Each one there was a character from the comics.

Havok is Cyclops' father
Given that age difference there would have to be with the former showing up in First Class, and the fact that poor Slim can't get no respect from the movie powers-that-be, why not? This is assuming that First Class is supposed to be in continuity with the other films, that is.
  • Well, there are siblings with 20+ years age difference. Examples: Axe Cop. And me too.
    • This isn't a case of 20+, this is 40+ years. Its physically impossible for them to be brothers.

Charles Xavier will lose all his hair in X-Men: First Class.
I mean, he appears in the movie with a full head of hair. There are two ways that he could lose his hair.
  • He will use his telepathy to a degree for some reason that he will become prematurely bald.
  • Magneto will attack him, crippling him and making him lose his hair.

The reason why Xavier in X-Men: First Class still has hair long after developing his powers...
Is that this isn't the same universe as the other films. The canon reason why Xavier is bald in the comics is because his hair fell out when he developed his powers. The same goes for the first four films, but the First Class film shows he has both powers and hair. That's because it all takes place in a world where his powers didn't affect his hair as well as all the other continuity changes.
  • Or, alternatively, it shows that his powers haven't fully developed yet, which would explain how he goes from holding one person still—Shaw—to an entire museum full of people in X2.

Beast is Nightcrawler's father.
This isn't my theory, it's here (post by pikahyper). Here's the logic:
"[...]at first I thought they were throwing Beast into the mix in an attempt to make it harder to figure out who Nightcrawler's father is but then I thought no cause it would be too obvious still since Azazel is a teleporter and then it dawned on me... what if Beast really is Nichtcrawler's father and Azazel is Mystiques father, big change from the comics but that isn't new. So teleportation could be an inherited trait for the men in Azazel's bloodline and that is how Nightcrawler got it and then he inherited the blue coloring, fur and demonic features from Mystique, Beast and Azazel"

Darwin is still alive.
So Darwin was killed by Shaw in this movie. His powers were essentially "not dying", but he died anyway. Or did he? In the comics, he survives something similar by converting himself into energy. It's even a part of his origin story! In the movie, he first turns into a metallic substance after being attacked by Shaw, then into something resembling rock or gravel, and then we don't see much more. It's obvious his body was trying to find different ways to survive the excess energy. Afterwards, the rest of the team say they don't even have a body to bury. Sounds similar? Darwin may well have pulled off that trick in the movie, too.

Darwin is still out there somewhere.

  • He didn't just survive, he evolved into a more advanced life form.
  • Shaw has rules against mutants killing other mutants. If he knew Darwin could survive, then he might not be as much of a hypocrite as he seems.
  • Plus no body, hence being unable to bury him. I think his body is going to reassemble itself down the line it may take decades. Imagine his reaction when he finds out what the rest of his classmates including Eric got up to since his time away.

The entire Cold War plot of First Class is a part of an enormous Batman Gambit by Ozymandias.
In this alternate timeline, Ozymandias is active in 1962 as opposed to 1984, and Dr. Manhattan does not exist (probably because Dr. Osterman didn't have his accident). So, in order to prevent a nuclear war between the USSR and the USA, he decided to give them a new common enemy: mutants. And Sebastian Shaw is the prime Unwitting Pawn in the gambit; his objective is to create a sense of mutant threat, then be disposed of by fellow mutants.

Meanwhile to the finale of First Class, Nikolai Sokolov has just been returned to Russia, in exchange for removing the missiles from Cuba, where he will be forced to continue development of the Shagohod. Two years later, Naked Snake is dispatched to Tselinoyarsk to retrieve him, starting the Virtuous Mission.
The End (a plant dude), The Pain (some sort of animal empathy?), The Fear (super double-jointed-ness), The Sorrow (spirit medium), and Volgin (electricity powers) are mutants, which would explain their totally-unexplained-in-game powers. The Boss is just a super Badass Normal (or related to Captain America somehow?). Sebastian Shaw is a former member of the Philosophers who wants to destroy both the US and USSR in an If I Can't Have You moment with regards to the Legacy. Both Metal Gear and X-men have genetics as a major theme, so a connection is possible.

  • Somehow, I just can't see Nightcrawler's rampage through the White House being quite so one-sided if that were the case. "George Sears'" pseudobiography placed him as a Navy SEAL during Desert Storm and later Somalia, Serbia, and Kosovo. (I know, by the Regs he would have been too big and tall for them, last time I checked, but Kojima's making this up, not me.) And besides that, he's #^9|{ing Solidus Snake! After something like that, there's no way the Patriots wouldn't have gotten to Stryker first after undermining their chosen candidate like that.
    • Especially as the Weapon X program Had to have gone on with at least the tacit consent of the Patriots. For that matter, they would definitely have canceled Stryker [[in the spy novel jargon sense of the word]] right after Three Mile Island. That would have been cutting it far too close to something like the Big Shell Incident thirty years early!

Xavier didn't actually erase Moira's memory.
She is just pretending in order to mislead the CIA.
  • Personally, I like to think he restored her memory immediately afterwards. She was probably (justifiably) mad at him for a while, but eventually accepted his reasons. That way, erasing her memory without permission doesn't seem so much like mild mind rape.

Shaw/Schmidt injected First Class!Erik with shark DNA at some point.
He was trying to find out if combining Erik's magnetic powers with shark genes would create a human with a shark's electrical sensitivity. Results overall were unimpressive, but there were some minor cosmetic changes.

Sunfire will factor in the sequel
In the original comics, he was attacking Washington after his mother died from fallout of Hiroshima. It'd be more plausible for him to appear than the modern movies.

Magneto never lost his powers in The Last Stand
Earlier in the film he showed his Auschwitz number and said that no needle would ever penetrate his skin again. Take notice that his clothes are padded rather thickly and though he could not prevent the needle from entering at all as it's not made out of metal, the hypothetical padding explains the moving chess piece at the end, as he was feigning his powerless form.

X-23 will be played by Summer Glau

If she appears in a film that is. You know it makes sense.
  • Psh, it more than makes sense, it's downright eerie watching Firefly if you've read the X-23 miniseries first...I have to keep reminding myself that's not Laura onscreen.

Dave Barry appears in the second Origins film involving Wolverine.
In Dave Barry Does Japan, he comments that a Japanese energy drink tastes like wolverine spit. The drink is called Hugo. Wolverine is played by Hugh Jackman (there are many readings for the syllable "go", many of which could be euphemisms for kissing or references to Wolverine). In one of the post-credits tags for Origins: Wolverine, he is in a Japanese bar, implying that his Japan-locale personal series takes place here. Dave Barry often encounters embarrassing situations, and Wolverine can always use the spare bit of humor to lighten an otherwise totally-awesome-but-lacking-rules-aside-from-cool fight, and what better way than trying to Midbattle Kiss the love interest and accidentally planting one on a sixty-year-old male American tourist?

Wolverine was Van Helsing in the past
He's played by Hugh Jackman, was turned into a werewolf, and seems to be immortal. By extension of course, Wolverine has also been a cattle drover, a magician, and a musical star.

The next X-Men movie should be...
X-Men: Apocalypse. I'm thinking Tony Todd as Apocalypse, Clive Owen as Mr. Sinister, and Michael Biehn as Cable (among other ideas).
  • I can totally see either Tony Todd or Clancy Brown as Apocalypse. Or maybe Clancy would work better as Cable. Gary Oldman as Sinister.
    • Jonathan Frakes as Cable. Gary Oldman will be playing Judge Dredd in a Dredd movie that doesn't actually suck.
  • Confirmed. After Days of Future Past, the next movie will be X-Men: Apocalypse.

X-Men Origins: Wolverine was actually a Danger Room scenario based on Logan's speculation about his missing memories.
It's not his fault. He's the best there is at what he does, and what he does isn't writing.

Stryker knew about X2 in X-Men Origins.
He captured Deadpool, a mutant who can break the fourth wall. Deadpool then told him about X2 and Stryker realized that he had to set that movie in motion. This explains why he spent so much money on giving Wolverine the Adamantium when Wolverine would probably turn against him anyway. This also explains why he continually tried to erase Wolverine's memory. Soon, Stryker found out that he dies in X2 and decided to destroy the X-men continuity, forcing the produces to have a reboot. Deadpool went along with this, knowing that he might actually have a part in the new reboot, but when he saw the fight scene between Wolverine and Gambit, he realized that this movie could never surpass the old X-men films. He tried to warn Stryker that the movie was getting stupid, but Stryker sewed his mouth shut. Angered by this, Deadpool decided to sabotage the movie by killing its main characters, thus forcing them to reboot X-Men Origins and give him his own movie. And the crazy thing is, it worked

Kayla did not die in X-Men Origins: Wolverine
The character Kayla was based on had healing factor in the comics, so her movie self probably did too and she eventually recovered from her wounds.

Mariko Yashida will be played by Chiaki Kuriyama in the next Wolverine movie
This will make a lot more sense if you've seen the movies she's been in besides Kill Bill.

Even after his spinal injury, Xavier can still walk for short periods of time using his psychic powers.
He is able to engage in telekinesis as well as telepathy, but using telekinesis to make himself walk is extremely taxing, so he can only do it for a few minutes at a time.

This universe has more than one Sabertooth.
In other words, the character played by Liev Schrieber is an entirely distinct individual from the one played by Tyler Mane. The powers are different, the fighting styles are different, the hairstyle is different (notice that Liev Schrieber's Sabertooth never really changes his appearance even though he lives for over a hundred years), and Tyler Mane never makes any reference to their past (in fact, he barely talks). For that matter, Tyler Mane is bigger than Liev Schrieber.
  • More then likely the case as Victor Creed in Origins is never once referred to as Sabretooth and is an amalgamation of two separate comic book characters, Dog Logan and Sabretooth. so in this universe Victor Creed is Logan's brother but not the mutant known as Sabretooth. Another possible explanation for keeping them the same character could be Hank McCoy's formula that accelerated his mutation turning him into Beast. Both Magneto and Mystique are aware of the formula and it's effects, and Mystique was part of Hank's brainstorming sessions when designing it. So it's possible that after hooking up with Magneto and the Brotherhood, Victor was given the formula and his changed appearance is the result.

That cowardly extra in First Class who tells Shaw to take the mutants and let the "normal people" go was being forced to do so.
Shaw wanted the young mutants to join him against the humans, so he put a gun to a security guard and told him to loudly state his mutant prejudice, to convince them of humanity's evils. This explains why it sounded so much like Bad Bad Acting.

Methos was in X2 to keep an eye on Stryker and to make sure he never found out about the Immortals.
I'm just saying.

After First Class Azazel will rape Mystique, Magneto will kill him and Mystique will give birth to Nightcrawler and abandon him, because he looks much like his father.

The fourth X-Men movie will reveal the current relationship between Iceman and Rogue.
Bobby doesn't appear to be happy with Rogue's decision to take the cure, even though she did it for the both of them. But they may have grown apart by the time the fourth movie (if ever) occurs.

The films are in the same universe as Mystery Science Theater 3000
They're both set in the "not too distant future"...

The unnamed CIA "Man in Black" from First Class was...Richard Parker.
Aka, the father of Peter. Think about it...known CIA agent, involved in deep-black intelligence work (as in the comics); surprisingly personable and responsible when dealing with these new powers; tragically murdered, with superpowered kids not being there to save them...

Granted, the theory doesn't really work with existing (movie) continuity, due to rights and timeline issues, unless you screw around with canon until the universe is a de-facto or an outright reboot...in other words, considering these are Marvel properties, a perfect match!

Between First Class and the events of Wolverine, Beast developed a treatment to heal Xavier's spinal injury
With the accidental and unfortunate side effect of making his hair fall out.
  • Then why is he still in a chair by X1? Unless, he's just faking it...
    • Projecting the image of a wise cripple to make people listen him isn't really out of character.

Magneto's machine from the first movie enhances a mutant's powers
So Cyclops mentioned in X2 that Jean started getting all phoenix-y after the first movie. Also notice how Wolverine goes from taking several seconds to heal minor cuts and wounds in the first movie to being able to instantly regenerate most of his skin and flesh while Phoenix is trying to disintegrate him in X3. Best guess is that Magneto's machine not only made regular humans into mutants, but enhanced the powers of existing ones.

Omega Red is based on Andrei Chikatilo.
Russian child murderer first introduced about the time Chikatilo was caught? Hmm... He was even executed in a similar manner to Chikatilo, but I don't know if this was revealed before or after Chikatilo's death.

Michael Fassbender will show up to play Joseph.
Joseph is a younger clone of Magneto.

The third "First Class" movie will end with Xavier using a new Cerebro to make everyone forget that the mutants exist.
However, this will strain him so much that he will go bald, and it will also influence his memories, which will explain all the errors in his introduction to Wolverine in the first movie.

In The Wolverine, the Jean Grey we see in Wolverine's dreams is actually the Dark Phoenix.
Self-explanatory.

Sabretooth looks different because Magneto tested his machine from the first movie on him
To be sure that the radiation had no effect on mutants. It actually triggered an enhancement in his mutation.


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