The X-Men have been a persecuted class of citizens in Marvel Comics since time immemorial. However, their existence next to other heroes like Iron Man, Spider-Man and Captain America has always begged one question: Why are non-mutant heroes, who live their lives exactly as mutants do, treated better and even celebrated, while the mutants are actively lobbied against in every institution on the planet?
The Marvel Cinematic Universe is uniquely positioned to address this issue or create a scenario where such a dichotomy makes narrative sense. Currently, as the MCU stands, any off-word species has been labelled a threat by the United States government. This includes beings from other planets, like the Skrulls, and immigrants from other dimensions, like the Clandestine. Also on the list could be Asgardians and other races associated with them (like light elves and dark elves).
This could play into the fact if the MCU follows the Arrow-verse when it comes to streamlining their multiverse, post Avengers: Secret Wars.
Avengers: Secret Wars might reorganize the Marvel Universe
The Marvel Cinematic Universe has mostly been dominated by non-mutant superpowers entities. Mutates, aliens, androids and super-soldiers have all been part of the mainstream, while a few mutants have been introduced in recent entries of the franchise. While Namor and Kamala Khan are the only mutants that exist in the main MCU timeline so far, mutant characters have been introduced as part of other timelines and universes, such as Earth 838, where Charles Xavier existed as a part of the Illuminati and Hank McCoy who made a cameo in the post-credit scene of The Marvels, where Captain Monica Rambeau is stuck in another universe.
Given that the mutants were absent from all major conflicts on Earth-199999, it is safe to assume that versions of the main team of X-Men do not exist in the main MCU timeline. Therefore, the only way these characters can share screen is if there is some sort of multiversal crossover, such as Avengers: Secret Wars. However, post the film, it would be in Marvel’s best interests to have the characters of these different factions (The Fantastic Four, Avengers and X-Men) share a continuity, to avoid future crossovers becoming a retread of the Multiverse Saga.
This would require an internal narrative that could reorganize the various universes into a single timeline, one where mutants can coexist with other superpowered characters. Of course, if this were to happen, it would be without the consent of authorities on planet Earth, possibly causing a situation much like The Blip.
The X-Men could be dimensional immigrants
As the Marvel Cinematic Universe sees itself organized into a single dimension, Secret Wars could make good on its promise of being a soft reboot, introducing s to a world where mutants coexist with other heroes.
However, the people of Earth might be aware that the mutants come from different dimensions, and with President Ritson’s protocol for off-world species still in place, the X-Men and mutants at large could find themselves persecuted., while other “indigenous” heroes might be celebrated by the masses.
While Secret Wars could see other alien entities return to their neck of the universe, the mutants, with nowhere to go, might see themselves caught in an unsavory situation. However, given that the dimensions would be melded together, there would be nowhere to go, putting them on a planet, that is essentially their home dimension, but still different and alien enough that the general masses would not be able to digest them as part of their daily life.