The X-Men are clearly the biggest aspect of all this, not only because of their stable fanbase and cinematic success, but because of the sheer number of characters involved in the X-brand. We’ve seen maybe 75 different mutants appear in the X-films to date, which is like a nickel next to a stack of hundreds compared to how many mutants exist in the comic books. Before Disney and Marvel Studios start worrying about introducing Boom-Boom or Doop (please, God, introduce Doop), however, they have to figure out how to fold the X-Men into a world that already knows the Avengers.
Since X-Men: First Class rebooted the franchise in 2011, mutants have been inextricably connected to world events like the Cuban Missile Crisis or that time Magneto tried to assassinate President Nixon. It would be inconceivable to simply add that mess to the MCU timeline, a universe in which superpowered beings didn’t really start emerging until the late 2000s. Yes, Captain America: The First Avenger was set during World War II and Captain Marvel will take place in the ’90s, but you can’t expect audiences to buy that Nick Fury only started trying to recruit remarkable people in 2010 when the X-Men were literally stopping the Apocalypse in 1983.
So, if you can’t simply say, “the X-Men were here all along,” what do you do? One answer would be the multiverse. Agents of S.H.I.E.L.D. recently started fiddling with the concept, and both Ant-Man and Doctor Strange have already brought multiple dimensions into the conversation. If you really wanted to keep the current cinematic X-Men class alive in the MCU, ripping a hole through the space-time continuum might be a way to do it.
Ultimately, however, that would be a ridiculously complex path and likely unsatisfying. Time travel in the X-films has already made continuity a mess, and bringing in universe travel wouldn’t help matters. Besides, Hugh Jackman’s story as Wolverine ended beautifully with Logan (poor guy will never get that X-Men/Avengers crossover he wanted so badly), and though X-Men: Dark Phoenix was intended to launch a new trilogy, it’s probably a perfect way for the current incarnation of the X-Universe to end. So, perhaps it’s best to go the way of Spider-Man: Homecoming and go for a full reboot.
That way, you could sneak Wolverine into WWII with some nice retconning, lining the character up with Captain America just like in the comics. You could even have the sudden rise of mutantkind lead to an adaptation of the infamous Avengers vs. X-Men storyline — essentially the Civil War of team crossovers. (In the comics, it’s the return of the Phoenix Force that sparks the discord, but even if Dark Pheonix sucks, I don’t think audiences need a third adaptation of that story.) Imagine if the first X-Men MCU film pits a newly formed team against Magneto’s Brotherhood (movie one); in the destructive wake of the final battle, the Avengers are sent in to assess the threat (movie two). Misunderstandings and pride arise, and you’ve got two giant teams of heroes duking it out. After the Sokovia Accords, the characters’ internal conflicts would be even more heightened. Once the dust settles, you could have Beast, Wolverine, Storm, Rogue, or any of the other X-Men who have historically also been Avengers switch teams (movie three). Scarlet Witch could even do the reverse (we’ll get there, folks).
It would have to be something that sets the rise of the X-Men parallel to the formation of the Avengers, just tucked in the background. Heck, maybe Professor Xavier actually gets inspired by Nick Fury. But there’s actually one character who might have already set that groundwork. A character whose story could be used as an anchor to lock both established universes together.