Hmm...yeah, I’d like to see something like Spider-man Homecoming which avoids the origin story altogether and just hits the ground running. I still say a loose adaptation of Night of the Sentinels, the two parter that kicked off the 90s Animated Series, combined with the Mutant Massacre would be the perfect way to reboot the X-men in the MCU. You start with the POV character, in that case Jubilee, finding out she’s a mutant and being hunted by Sentinels. The X-men step in, save her, and you find out who they are when she wakes up at the mansion and escapes. As “Alice” tumbles down the proverbial “rabbit hole” here, she discovers this whole world right under her nose, where mutants are openly hunted and rounded up and forced to register with the government. In many cases they end up in camps if the government deems their powers dangerous, which happens more often than not. And yet most of the American public and even people around the world are oblivious to it. Those who know, turn a blind eye.
Later, this kind of evolves into a murder mystery where mutants are being massacred in the tunnels beneath NYC, where they’ve established a kind of colony where they can seek sanctuary. Of course, this leads to the Marauders and Sinister as the big bad of the film, but the Mutant Registration Act, Project Wideawake and the Department of Mutant Corrections (DMC) run through the film as undercurrents, establishing this sub-world we suddenly find ourselves in within the MCU, which is very dark and certainly not the kind of thing the Avengers would condone if they were aware.
You also have to establish where mutants have been and why they’re just now showing up, of course. Why doesn’t, say, Captain America know about them? I think there could be a cool flashback scene at some point, maybe not in this film but in a future one, where Logan and Rogers meet and realize that they met during WWII...but that’s probably best saved for later. At any rate, if mutants have been around, why is the public just now finding out about them? There are several options, but here’s the one I really like as it plays on House of M and also incorporates some cool stuff from the Ultimate Universe where mutants were actually a government experiment spinning out of WWII, much like Captain America...
- I’d have it so that X-gene mutations in humans, which produce superhuman powers, have existed in a handful of cases throughout history. En Sabah Nur, Selene, Gideon...in fact, many select figures throughout history (Genghis Khan? Abraham? Jesus Christ?) may have been mutants. They have the pure form of the X-gene.
- During WWII, while the Allies were focused on the Super Soldier Program which gave us Captain America, the Nazis were obviously running their own experiments. In one of these, they took cells from a man who couldn’t be killed (Logan), who some German soldier had encountered at the Battle of Verdun in WWI and written about and later a Nazi spy somehow obtained samples of this man’s blood; and they tried to replicate his X-gene. Many people injected with it died, but it was successful in the case of one young boy, Erik Lensherr (Mutant Zero).
- From there, many suspect due to the atomic bombs being dropped at Hiroshima and Nagasaki and the onset of the nuclear age, this new form of the X-gene took off rapidly, showing up in a great number of births from the late 1940s onwards. This caused a lot of panic throughout the decades, first in the 60s as more and more reports of mutants started to surface, and then through the 70s and 80s; until finally, after the end of the Cold War, an agreement was reached by major world governments to erase the mutant threat.
- They turned to a mystic named Magda, who had been in the employ of the Kremlin for many years, and broadcast her spell across the world using their satellites; which stemmed the flow of mutant births to almost nothing and wiped the minds of everyone on the planet in terms of even remembering the mutant menace. So mutants were all but forgotten. A few did remain, however, and Charles Xavier was one of those. For years, in secret, he has been harboring the few and far between mutants who popped up. And SHIELD, of course, was aware of this and supported his efforts to safely contain mutants and train them in the use of their powers, so long as he kept them hidden from the world at large.
This kind of establishes Charles as “in the know”, which will be important when we get to the Illuminati and Secret Invasion for the next MCU phase.
Now, after whatever happens in Avengers 4, however, something has caused mutant births to tick back up again. And this has led to the United States and other world governments launching Project Wide Awake, in secret, and unleashing the Sentinels. As more and more stories are popping up about mutants and this secret program which employs giant mutant hunting robots to contain them, the world has finally gone public again regarding “the mutant menace” and the United States Congress has passed the Mutant Registration Act. This is essentially where we find ourselves at the start of “The Uncanny X-men”, which would be the first X-men film in the MCU (unless you count Deadpool and X-Force as already being in the MCU, which I would).
Okay, that’s enough. Just a few crazy ideas. But something like that could work IMO. It sets up this dark underside to the MCU which mutants have to exist in, explains where they’ve been and why no one really knew about them until now, and has this major conspiracy element to it that unravels which gels nicely with Secret Invasion and the conspiratorial tone of that, should that be the next big MCU phase. In fact, it could later come out that highly placed Skrulls within world governments were behind the “erasure” of the mutants on M-Day so that humanity wouldn’t have a super powered populace to fight them and their subversive takeover of the Planet Earth.