The X-Men are due to arrive in the Marvel Cinematic Universe (MCU) very soon, but one plausible explanation about why they haven't appeared until now was ruined thanks to Secret Invasion. Back when the MCU began in 2008, the rights to use the X-Men characters in film and TV did not belong to Marvel. Years earlier, when the publisher was struggling, it chose to sell the characters' film rights in order to stay afloat. However, when Disney bought Fox, the rights returned to Marvel.
However, this created a challenge for how the MCU could then introduce mutants and the X-Men team, especially considering the characters' rich history. For example, Magneto and Professor Charles Xavier are two mutants who have many years' experience using their powers before they go on to form teams of mutants. But there is one fan theory that could go a long way to explaining where the mutants have been in the MCU, because this idea was already wasted on the Skrulls in Marvel's worst TV show to date.
The MCU's "Hidden In Plain Sight" X-Men Theory Explained
The X-Men Need To Make Their Debut In The MCU
The "Hidden in Plain Sight" theory appears to have originated about three years ago when a Reddit , jadamsmash, proposed how the X-Men could be folded into the MCU. Essentially, they believed the X-Men, or more accurately, the mutants, had already been in the MCU for generations. However, these mutants had clear tension with humans when they first appeared, and this likely came to a head around the time of World War II. After a major fallout between humans and mutants, a powerful mutant, likely Charles Xavier, wiped the minds of humans around the globe with Cerebro to protect mutants and hide them from the world.
In this way, Charles could then find other mutants when they manifest, bring them to his secluded school for mutants, and allow the world to go on unaware of their existence. Presumably, when these mutants finish their education, they could integrate in society, concealing their powers, and live peaceful and good lives. Potentially, some mutants would find love with each other, and they could live a quiet life together, while some others may grow tired of hiding, and that would be where a figure like Magneto steps in to provide them with another choice, and take mutants to a place like Genosha, where they could live free without humans.
Why The X-Men's Hidden In Plain Sight Theory Is Too Close To Secret Invasion
Secret Invasion Already Introduced A Civilization Integrated With Humans
The issue is, since this theory was put forward, Marvel released Secret Invasion. Secret Invasion reveals that not only did the Skrull's arrive on Earth in 1995, but since that time, the Skrulls have been present on Earth, hiding their true identities, and living among ordinary people. While it is reasonable to assume that this wild possibility of an entire group of people being hidden among the general population could happen once, it would be ridiculous to try and apply that logic twice in the same universe.
And while the Skrull narrative played an important role in Nick Fury's story, and it helped to create an additional tense storyline for the Multiverse Saga, it does appear that it ruined the chances of something like this working again for the mutants. As a result, Marvel will likely need to find another explanation for why the mutants have been silent, and what causes them to crossover into the stories now. Especially since there are so many points where the mutants may have been inclined to reveal themselves and help, such as in the final conflict in Avengers: Endgame.
How Else The MCU Can Explain Where The Missing X-Men Have Been
There Are Other Options For Bringing Mutants To The MCU
Fortunately, there are several other routes the MCU could choose to apply when introducing the mutants and establishing why they did not appear until now. With the comics having not just one but two independent mutant civilizations, Krakoa and Genosha, where mutants were able to live free of humanity, this could be one option for the MCU. And, considering kingdoms like Wakanda and Talokan have already proven that determined and powerful people can hide their existence from prying eyes, it's possible that the mutants have avoided detection in this way too.

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Otherwise, the obvious answer comes from the Multiverse Saga. Key mutants may never have lived in the Sacred Timeline until the events of Avengers: Doomsday, and Avengers: Secret Wars see them crossover. Mutants have been confirmed to exist in the MCU, with some heroes possessing their powers thanks to their mutant genes, but when it comes to heroes like Professor X, Deadpool, and Wolverine, all of these characters exist in other realities, and have been seen interacting with the Multiverse. But however the MCU introduces the X-Men, it's unlikely they could have been hiding in plain sight.