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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.

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  • 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.
  • Or, since the next movie after Days of Future Past is going to be about Apocalypse, he will turn out to be saved by the titular villain and turned into a Horseman.
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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 may have also given 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
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blended into the shadows as one of her powers dictates. Also as a Psylocke fan, I want her back.
  • Confirmed to be alive in novelization!

X-Men 4 will be about Apocalypse
C'mon, how awesome will that be?
  • Jossed, 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.
    • Cyclops is roughly 16 in the sixth movie, so he would have been born no later than 1967. That's five years after First Class. 40? No.
    • X-Men: Apocalypse jossed this. They are explicitly stated to be brothers, although the twenty year age gap isn't addressed. Perhaps their parents had Alex around 18 and Scott in their late 30s.

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.
    • Jossed, although there are several Mythology Gags regarding his inevitable loss of hair.
      • He does lose his hair in X-Men: Apocalypse.

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.
  • He did erase her memories, and restores it at the end of X-Men: Apocalypse.

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.
  • Jossed. Laura will be appearing in Logan, and is currently reported to be played by Sienna Novikov (though some evidence suggests it will actually be Dafne Keen).
    • The role ultimately went to Keen. Novikov was one of the stun performers.

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!

  • Or Richard Parker's father. He looks to be in his 30s when when the movie takes place (in 1962), so he'd be too old to be Peter's dad. Plus, the wide time-gap makes him being Richard impossible, with either the Tobey Maguire!Peter born in 1984 or the Andrew Garfield!Peter born in 1995. The "Man in Black" may already have a family in the time of his death: a wife with two sons (Ben and Richard). Richard himself eventually works for the government like his father, and soon becomes a S.H.I.E.L.D. agent.

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.
    • Offhand, by X-Men: Days of Future Past, Beast had developed a treatment for Xavier's spine, which also shuts down his powers, which he took almost to the point of addiction. He still has his hair though.

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.

Emma Frost from Origins is a daughter of Emma Frost from First Class
And so is Kayla. One has mind-related powers, the other turns into diamond. First Class Emma has both.

Origins is what Wolverine is imagining in a bar.
One version of Origins has a credit scene depicting Wolverine sitting in a bar, saying that he is "drinking to remember." Everything up to that point was him trying to piece his memories together. Maybe he even drank a worm that made him hallucinate the entire thing. The bar scene could possibly be sometime after he met the X-Men, thus explaining the presence of Cyclops and Professor X in the story.

Apocalypse, the Big Bad of the next movie, will be played by Jason Momoa, the actor behind Khal Drogo
Because... Well, look how perfect this is!

Cable and Deadpool will be introduced/reintroduced for the Apocalypse movie
One, because Cable was important in the original Age Of Apocalypse storyline, and two, because Deadpool was (and is still) associated with that character. Given the backlash against Dudepeel, it'd be a perfect opportunity to fix the latter character and bring the former into the film series.
  • It has been stated that both of them will appear in X-Men spin-off film Deadpool, though.
    • Cable's a no-show in Deadpool. However, they did promise to bring him in for the sequel...
  • At least half-jossed; Deadpool's movie was released before the Apocalypse one.

The Wolverine takes place in 2007 or 2008.
According to the 25 Moments website, The Last Stand takes place in 2006. Hugh Jackman said on STAR 94.1 San Diego that The Wolverine takes place 18 months to 2 years after The Last Stand. That would mean that most of the movie takes place in either 2007 or 2008, with the post-credit scene that is two years later taking place in 2009 or 2010, just in time for Sentinels taking Xavier's school in 2010 according to the 25 Moments website.

Mystique has an additional limited precognition power.
She based her default "normal" appearance on a vision of a popular actress from the future.

The "cosmic being" seen at the opening of X2 is the Phoenix Force.

The next Wolverine sequel will feature either Daken and/or X-23
Because why the hell not?
  • Possible on X-23. The stinger of 'X-Men: Apocalypse'' has people from Essex Corporation enter the Weapon X facility and take Wolverine's blood. Many fans assume Mr. Sinister will clone X-23.
  • Confirmed. Dafne Keen is portraying X-23 in Logan.

Mystique never lost her powers, the whole thing was a set up
Magneto callously abandoning her after all those years together, not to mention she'd have made a wonderful symbol for what the humans would do to any mutant they considered a problem, is both stupid and out of character for him. However the information she gives to the authorities leads to a distraction and the only evidence she's lost her powers is her reverting to her more human appearance and staying there, easily faked. Remember, Mystique was exposed to Magneto's machine back in the first movie, the machine that seems to boost the powers of mutants and kills human. I suggest Mystique gained enough control over her body to expel the cure from her body without it affecting her, and the whole scenario was set up by them in advance.

The next Wolverine movie will be an adaptation of Wolverine and the X-Men
It is a highly popular comic and features Wolverine as a teacher and at times as The Heart of the team, something that he's grown into by the time of the DOFP movie. It can also tie directly into the previous film, what with the young reincarnation of Apocalypse being a major character.

Decimation and M-Day happened in the original timeline
This is why Magneto is such as Jerkass and had such a callous treatment of Mystique when she was depowered. Being a Holocaust survivor, seeing mutantkind being nearly extinct during Decimation and after witnessing a second attempt at mutant genocide by Stryker, Magneto became even more determined to obtain mutant prosperity.

Mr. Sinister will appear in X-Men: Apocalypse.
As Apocalypse's Dragon, or even Dragon-in-Chief. His name was shown in X2 while Mystique was in the computer searching for Magneto; and his only other appearance was in the non-canon video game X2: Wolverine's Revenge. So this would be a good a place as any for him to finally make an appearance. He may also be a Dragon with an Agenda, if his own goal involves a young Cyclops and young Jean Grey.
  • Confirmed, sort of. The Stinger implies he will be the antagonist of the next film.

The next Wolverine sequel will feature Professor Thorton/Hudson.
He will be revealed to have been hired by Stryker to lead the Weapon X experiment. His only other appearance was in the non-canon video game X2: Wolverine's Revenge.

Sabertooth will appear in the next Wolverine sequel.

Banshee will return as a Horseman in X-Men: Apocalypse.
Partly because he was one in the comics, and mostly to confirm him as the father of Siryn who appeared in X2.

Magneto's behavior in X3 is due to an off-screen Villainous Breakdown
Let's look at what the whole setup to X3 is: a "cure" for mutation has been found. That, right there, is a huge upset to Magneto's position. Even if directly hostile human bigotry, the sort that would provoke a "fight back" reaction would scale back, human bigotry can now subtly pressure mutants to depower themselves to "fit in". Furthermore, a cure also provides an easy, appealing, safe alternative to mutants; they can just take a dose and go right back to their old lives, blending in with the rest of baseline humanity and not have to struggle and fight for the right to be mutants. This robs Magneto's mutant rights/supremacy movement of a lot of its attractiveness. If humans can weaponise the cure — as they do — then that means that they have a weapon against mutants who do decide to fight against human oppression.

Then there's the philosophical shock; Magneto has always believed in the idea of mutants as the next phase in human evolution — his whole philosophy is based on the foundation that mutants are destined to replace humanity. But this "cure" works. It can undo what Magneto saw as inevitable. Implying that mutants may indeed be what so many humans have derisively called them; nothing more than an aberration, a blip on the evolutionary chain, the equivalent of sickle cell anemia or colorblindness. That right there is a massive upset to Magneto's beliefs. The sort of thing that can drive anyone a little loopy.

The Dr. Shaw in X2 is Shinobi Shaw.
The novelization referred to him as Sebastian Shaw, so he could be Sebastian Shaw, Jr. in this universe.

All the continuity errors and plot holes between the movies can be explained.
Logan isn't the only time traveler in the movieverse, He's just the only one we see on screen. The comics have so many time travelers; Bishop, Cable, Rachel Summers, Trevor Fitzroy and Legion just for starters, that at least a few must exist in the movies (and perhaps will be seen in Apocalypse.) The constant meddling of time travelers from the future causes the movieverse to exist in a constant state of flux with all the changes only being noticeable to the audience.
  • Confirmed: it’s Deadpool

The mooted X-Force movie will be a direct sequel to X-Men: Apocalypse
It'll draw from the first few arcs of the 2010s Uncanny X-Force series, which were about a team including Psylocke, Archangel and Deadpool attempting to hunt down Apocalypse's followers before they succeed in resurrecting him. In the film version of this story, these three will be brought together by Cable instead of Wolverine. Early reports indicate that Psylocke and Archangel are going to be among Apocalypse's horsemen in this movie, which will give them a personal reason to hunt him down.

Other possible team members:

  • Colossus. Confirmed for Deadpool, and he was a member of one of the more recent incarnations of the team.
  • Domino. Simply because she's frequently found somewhere near Cable.
  • Juggernaut. They initially wanted him for X-Men: Days of Future Past, which suggests they're keen on bringing him back.
  • Nightcrawler. Again, a version of him was part of one of the recent incarnations of X-Force, and he will be established in X-Men: Apocalypse.
  • Negasonic Teenage Warhead. Either continuing to accompany Colossus, or having found a much cooler mentor in Deadpool.

The events of X-Men Origins: Wolverine are fake memories.
At some point between The Last Stand and The Wolverine, Logan started searching for his past again. He recovered some memories which were based on real events, but were highly distorted, and he accepted these as real. This explains how he seemed to remember Kayla in The Wolverine, as well as all the continuity errors between Origins and the other movies. He might have recovered some real memories at the same time, which would explain how he remembered Yashida.

The X-Men film that was set in the 1990s was going to be...
X-Men: Days of Future Present
  • Everything is closer to the comic storyline on annuals.
  • X-Men: Dark Phoenix will take place in 1992.

Fractured Timeline
The temporal machinations of Days of Future Past didn't just create a new future. It completely shattered the timeline altogether. Legion and The Gifted are known to each be set in their own alternate timelines from the core films (at least The Gifted is confirmed, Legion is deliberately ambiguous as to whether it's part of the film universe or not). Logan is established by Word of God to be set after the New Future from the end of Days, which explicitly sets it in the same timeline as Apocalypse. The Deadpool franchise is less clear, not helped by Wade's Fourth Wall breaking powers making him aware of there being two Xaviers. Thus, Days of Future Past has created a multiverse. At some future point there will be a Crisis Crossover leading to every franchise in the XCU having to come together when this multiverse is threatened.

Even after the 20th Century Fox buyout, the Marvel Cinematic Universe and X-Men universe's timelines will still be kept in alternate dimensions to each other.
Just to cut down on massive retcons (especially regarding the Maximoffs) and so both franchises can stand on their own.
  • Then, after more synergy has been built up behind the scenes, there'll be a crossover featuring a few characters from both franchises, likely ones who are major players by the time it's made, crossing into each other's worlds to fight Mephisto (being supernatural, he could access both universes via limbo or something).

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