Disclaimer [This story is now not solely set in the MCU, but will have small sections that could tie it in. So please, read the actual before judging. If you wish to not include this into the MCU, then please proceed to pt. 3]
By now, many fans of the Marvel comic book films have seen and most likely been aggravated with the film X-Men Apocalypse that 20th Century Fox released last year. Many fans of the Marvel characters were not happy that many things didn't come over into the film. However, this time I will not be talking about how X-Men Apocalypse could have been made into a better film, instead I will be going over the whole franchise as well as how they could be introduced into the Marvel Cinematic Universe, a.k.a. the MCU.
To start off, X-Men holds a very special place in my heart as not only was it the first ever Marvel movie I saw as a kid, it was the first time I had ever heard of Marvel or a Comic Book. In that regard, it really hurt when after the second film to see the franchise spiral out of control.
Now to begin, how to introduce the X-Men into the MCU. Now this part is mostly done out of fun and a desire to see the X-Men join up with the MCU characters. I don't see Fox ever handing the rights over after the successes of Deadpool (Fantastic Four on the other hand I do see them handing over)
So, how does one introduce the idea of Mutants in a world where there are no mutants? Many have thought up that perhaps they could exist in their own universe, and that they would be brought over in some way by Doctor Strange or the Infinity War. There is also an interesting idea in which the Scarlet Witch will do a 'No More Mutants' from the popular House of M story line at the end of Infinity War, but instead saying 'Mutants', thus bringing them into the world.
Instead, I see a much more simpler way to do this: Within the MCU there exists the race known as the Inhumans, who are a sub race of humans that were experiment on by an alien race. These Inhumans are not born with powers but instead gain them from the Terrigen Mist. Here's the simplest way to introduce Mutants; they are mutations of Inhumans who are born with their powers instead of needing the Terrigen mist.
These Mutants would therefore be the children of the Inhuman race, being a mutation in their genes that allow them to develop their powers at around their preteen years. Now, why are there not more of these Mutants? Simple, the probability of an Inhuman child being born with the X-Gene that makes them born with powers is very low, only around a hundred or so.
Now, you are probably wondering where are the X-Men in this. They disbanded before the events of Iron Man 1. See, one time frame that the MCU does not touch upon is the 80's - 90's. This would be an excellent spot to place when the Xavier's School was open and the X-Men were together. During that time a boom of Inhuman children were born with the X-Gene, but it was only around that time. Then due to a.) the Prof. dying or b.) the school being shut down, the X-Men were disbanded.
One reason I place the formation of the X-Men before Iron Man is the Avengers Initiative. In The Avengers film, the directors tell Nick Fury that the Avengers Initiative was shut down. Shut Down. They did not say 'Your Avengers Idea won't work' They said it was shut down, meaning there must have been a time when there were Avengers before the current incarnation. Now, who would have been these Avengers? Most likely candidates would be Ant-Man (Hank Pym) and Wasp (Janet Pym), due to them being from that time period. But who could've been the others? Could the X-Men have initially been candidates for the first incarnation of the Avengers?
Anyway, that would be an interesting way of saying that they were always there. So, the Xavier School was shut down and Mutant population dwindled, but due to the recent boom in Superhero activity, perhaps something reignited the X-Gene? And now the X-Men are needed once again.
Next will be the Cast in this new MCU version of the X-Men.