MCU"s X-Men Setup Secretly Began 11 Years Ago In Captain America 1

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Warning: This article contains SPOILERS for The Marvels
Summary

The X-Men were subtly set up in the MCU as early as Captain America: The First Avenger, with references to Alamogordo and super-soldier experiments with mutants.
The MCU has been slowly introducing X-Men Easter eggs, with Kamala Khan announced as the first mutant and Professor X appearing in Doctor Strange 2.
Beast's debut in The Marvels confirms that Fox's X-Men exist in an alternate reality and sets up future plans for the X-Men in the MCU.

Despite Beast's debut in 2023's The Marvels, the MCU actually began subtly setting up the X-Men, including Wolverine and Professor X, in the MCU all the way back in Captain America: The First Avenger. When Marvel launched the MCU back in 2008, they had to focus on superheroes who were, at the time, generally considered second-tier. All that changed when Disney acquired Fox's movie and TV assets back in 2019, and the rights to the X-Men and their associated characters landed at Marvel Studios.
Since then, the MCU's X-Men references and Easter eggs have steadily been drip-fed to the audience, with Kamala Khan announced as the first mutant, and Sir Patrick Stewart's Professor X notably appearing in Doctor Strange 2. So far, the MCU's X-Men movie remains intangible, despite a vague promise at Comic Con 2019 of future plans. Beast's appearance in The Marvels at least clarifies that Fox's X-Men exist separately in an alternate reality (though a different one to Multiverse of Madness' Xavier variant). But the start of this story kicked off way back in Phase One...
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Related The MCU Finally Confirms Where The X-Men Are 4 Years After Disney's Fox Deal With no sign of Marvel"s first X-Men movie, the MCU has finally confirmed the reason we"ve not met any of Fox"s mutants properly yet.
How Captain America: The First Avenger Set Up The X-Men

Surprisingly, there have been subtle hints of the X-Men since the MCU began. Released in 2011, Captain America: The First Avenger contains an easily missed conversation shortly after the death of Abraham Erskine. Captain America is presumed the only super-soldier, and an irate Colonel Phillips turns on him. "You're an experiment," he snaps. "You're going straight to Alamogordo." This is a deep cut in X-Men lore; in the comics, Professor X's father, Brian, worked at what was initially believed to be a nuclear power plant in Alamogordo, New Mexico, but his son eventually learned it was a government black ops lab experimenting with super-soldiers — particularly, with mutants. This fits perfectly with Colonel Phillips's comment to Rogers.
The experiments at Alamogordo remain a mystery even in the comics. Professor X eventually learned the facility was run by a scientist named Nathaniel Essex, an alias frequently used by X-Men villain Mr. Sinister, who was a twisted geneticist who hails from Victorian London and excels at genetic experimentation. He worked alongside Brian Xavier, Professor X's step-father Kurt Marko, and even the long-lived mutants Mystique and Destiny. There, they conducted the first experiments upon mutants. There were even ominous hints Brian Xavier was involved in establishing the Weapon X Project, which was responsible for coating Wolverine's bones with adamantium.

Captain America: The First Avenger Captain America: The First Avenger is a 2011 superhero movie starring Chris Evans as Steve Rogers, a weak patriotic civilian who becomes the test subject for the military's Super Soldier project. The film was the fifth film in the long-running MCU franchise and also starred Samuel L. Jackson, Hugo Weaving, Hayley Atwell, and Sebastian Stan.
Release Date July 22, 2011 Director Joe Johnston Cast Chris Evans , Hayley Atwell , Hugo Weaving , Sebastian Stan , Tommy Lee Jones , Samuel L. Jackson , Dominic Cooper , Stanley Tucci , Toby Jones Runtime 124 Minutes The MCU Has An Even Earlier Reference To The X-Men

As well as the Alamogordo reference, in The Incredible Hulk, Bruce Banner and General Ross' experiments into reforming Erskine's super-soldier serum also came with a huge X-Men reference. The project was officially designated Weapons Plus, a name obviously chosen to homage Weapon Plus, the clandestine government operation designed to create super-soldiers that lead to Wolverine's creation as Weapon X.
While Wolverine does not yet exist in the MCU, She-Hulk contained a reference to a mysterious figure brawling in bars with metal claws.
No doubt this and Captain America's nod were only intended as Easter eggs, even if they were so subtle they slipped past most viewers. But Marvel Studios could actually repurpose both now that they have the film rights to mutants and the X-Men, simply because it potentially serves as a setup for the latter. It would certainly explain how Nick Fury's wife was able to research the so-called "superhero gene" that seems to be the MCU's equivalent of the X-Gene. If that happens, Captain America: The First Avenger really will have helped set up that particular idea for the X-Men.
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