If there's one hangup with integrating the Fox properties into Disney's interconnected universe, it's the problem of introducing the X-Men — and the concept of mutants — after all this time, especially taking into account the long histories of characters like Wolverine, Professor Xavier and Magneto.
Agents of S.H.I.E.L.D. has called those with superhuman abilities "gifted," while Avengers: Age of Ultron — which introduced Scarlet Witch and Quicksilver, who are mutants in the comics — referred to the Maximoff siblings, byproducts of HYDRA experiments, as "enhanced."
Fans have spent years theorizing and coming up with potential ways to embed the previously Fox-controlled Marvel properties into the ongoing Marvel Cinematic Universe, coming up with ideas like:
The recent Marvel Comics event Secret Wars bridged the mainstream Marvel Universe (616) with other realities, merging multiple continuities into one as the 616 universe and the Ultimate universe collided.
Marvel Studios' upcoming Avengers: Infinity War and Avengers 4 may be the last big team up movie — at least for a while — making another super-sized cosmic event unlikely, but meshing two universes together could be a way to get mutants and the X-Men to make the jump to the Marvel Cinematic Universe.
It's even less likely this route would involve Fox's long-running X-Men franchise, as Disney — particularly Marvel Studios president Kevin Feige — will have their own plans for the X-Men that will be unrelated to Fox's almost twenty-years-old franchise.
Kang the Conqueror
One of Marvel Comics' biggest villains, Kang the Conqueror, has a history with the Avengers — but he's been off-limits to Marvel Studios because of his ties to the Fantastic Four, putting his big screen ownership underneath Fox.
With that caveat removed, the time-traveling Kang is free to show up to the Marvel Cinematic Universe — particularly if the Time Stone is used.
That particular Infinity Stone was introduced in Doctor Strange and will play a role in Infinity War, and the time-altering green gem could be used for the baddie to possibly pull some Butterfly Effect mumbo jumbo that leads to a disruption of the timeline, resulting in a world where mutants and the X-Men exist.
Marvel went to great lengths to establish the Inhumans as their replacement for mutants and the X-Men: with the X-Men's rights controlled by competitor Fox, Marvel had mostly ignored their existence, amping up the presence of the Inhumans in the comics and substituting them for the X-Men.
ABC's short-lived Inhumans didn't fare well with fans or audiences, but it expanded on the mythos introduced in Agents of S.H.I.E.L.D. Literally substituting mutants for the Inhumans would be a controversial move at first, but could be a relatively headache-less way for Marvel to give "natural" superpowers to a portion of the population.
The Inhumans mythology could be fudged to allow for the creation of mutants, giving rise to mutants — therefore introducing the concept of mutants and later the X-Men to the universe without too much cosmic number fudging.
Stan "the man" Lee is... the Watcher
Legendary Marvel Comics visionary Stan Lee has co-created much of the Marvel Cinematic Universe, and the creator appeared alongside the Watchers in Guardians of the Galaxy Vol. 2.
The Watchers — an ancient alien race of cosmic beings who are on hand for the galaxy's most notable events, but prohibited from interfering — are big-headed omnipresent know-it-alls who are often represented by Uatu, a character who has yet to appear in the Marvel Cinematic Universe because his rights belonged with Fox (being considered an ancillary Fantastic Four character).
Marvel already introduced the concept of the Watchers by way of a quick gag with Stan Lee, but the cosmic race could be used to introduce the concept of mutants — maybe as part of some kind of cosmic coverup? — that would widen the universe without too much over-explaining.
X-Men: Days of Future Past
As mentioned, Disney is likely going to forgo any and all of the X-Men franchise up to this point — excluding Deadpool, who was barely connected to that pre-established universe anyway — to introduce the X-Men fresh and anew into the Marvel Cinematic Universe.
In the comics, the Days of Future Past storyline pulled off some Back to the Future Part II timeline tinkering.
A possible sudden appearance by mutant and X-Men member Shadowcat could bring the revelation that the Marvel Cinematic Universe is a world without mutants — the result of some shady behind-the-scenes action that is later ultimately restored, "fixing" the timeline and seeing the return of a yet-to-be-introduced team of X-Men taking their rightful place in the universe.
It could be one convoluted and confusing retcon, admittedly, so it might be cleaner to use..
The Reality Stone
The Reality Stone — aka the Aether — was introduced in Thor: The Dark World.
One of the Infinity Stones, the gem has the ability to transform the universe — meaning it could be used to reshape the world, and create one where mutants (and thus the X-Men) exist.
Maybe the creation is purposeful, maybe it's accidental, but using a pre-established cosmic powerhouse like one of the Infinity Stones to recalibrate the universe would be a relatively clean way to introduce the X-Men — even it's an accidental byproduct of Thanos using the Infinity Stones in Avengers: Infinity War.
The concept of the Multiverse — or multiple, unrelated alternate realities — is a familiar one to comic book fans.
The Marvel Cinematic Universe is no stranger to the concept of the Multiverse, either: it was established in Doctor Strange and was recently set up in Agents of S.H.I.E.L.D., and with Infinity War likely to cause some cosmic tinkering, the events could lead to some kind of split in the Multiverse, resulting in the eventual emergence of mutants and the X-Men.
The reality of the Marvel Cinematic Universe could merge with another — not specifically Fox's now-defunct X-verse, but another outside reality separate from that one that houses the X-Men — making the X-Men transplants from another reality altogether. Marvel could look into a more grounded explanation, like...
Mutants were there all along
It's a bit The Sixth Sense-ish, admittedly, the revelation that mutants have been here all along and no one really knew, but mutants could be extremely rare and hush-hush. Maybe Nick Fury of S.H.I.E.L.D. knew about them, maybe he didn't. Maybe HYDRA has been experimenting on human test subjects for decades, inadvertently creating the mutant X-gene that then develops naturally in humans.
Mutants like Professor Xavier, Magneto and Wolverine could have been around a while — in the shadows — with a sudden emergence of the X-gene giving rise to new, young mutants like Cyclops, Jean Gray and Shadowcat. Someone like Logan maybe wouldn't know (or wouldn't care) how or why he has powers, or what a mutant is, or that he is one — he'd just be another "gifted" or "enhanced" who was somehow born that way.
The X-Men and mutants could then slowly but surely start to emerge from the shadows. This abrupt arrival of a new race of human — an evolved race of human — could even play into the idea why some people of the Marvel Cinematic Universe embrace "enhanced" superhumans like Captain America and Thor but are fearful of and hateful towards mutants and the X-Men.
When Doctor Stephen Strange took his first steps into sorcery, he saw some things, courtesy of the Ancient One.
Magic trickery — either involving Doctor Strange himself or at least the kind of magic introduced in that movie — could be a way to bring in the X-Men, even if some old school magic portal was involved.
There are "endless possibilities," after all, according to the Ancient One — it's not hard to believe there are mutants in at least one of those slivers of realities that audiences got a glimpse of in Doctor Strange.
The Fantastic Four
The Fantastic Four are known for their cosmic explorations and their galactic adventures.
Marvel could do the old two-birds-one-stone and introduce the X-Men through the Fantastic Four, with Reed Richards and his super-powered family going through some worm hole or alternate reality or cosmic portal or whatever that leads the way for a Marvel Cinematic Universe that now hosts the X-Men and the Fantastic Four.
The Marvel Cinematic Universe can now introduce and explore the concept of the Negative Zone — similar to the Quantum Realm explored over in Ant-Man and Doctor Strange — and all kinds of Stan Lee and Jack Kirby goodness can be brought into the universe by the Fantastic Four and their discoveries.