The X-Men are coming to the Marvel Cinematic Universe, and there are a lot of directions that the MCU could go. The most important thing is that Marvel does not follow the same storylines and themes that Fox has already tried. The Fox movies mainly took the direction of good mutants versus evil mutants, with the exception of the Days of Future Past movie, which was the only time it approached the real themes that Stan Lee and Jack Kirby introduced when they debuted the mutant team. Marvel needs to either go with the social messages or with their more sci-fi-based storylines to differentiate them from what came before.
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There are several X-Men storylines from comics that the MCU could use when they make their big solo debut after Avengers: Secret Wars.
7) The Mutant Massacre

This might be a tough storyline to start with, but if the MCU wants to have the mutants hit the ground running with the storylines that the general public hates mutants and fears them, the Mutant Massacre could be a great place to start. If the new Earth following Avengers: Secret Wars has mutants as an everyday part of the world, this could make them easy to fear. There is also a good argument that the X-Men should have Mister Sinister as the new big bad. It was Sinister who sent the Marauders to kill the underground mutant society, so this could show how deadly this villain really is.
6) X-Men: Schism

The big idea for the mutants is to bring in a young team and not focus on the veterans from the original films. This means no Wolverine, Cyclops, Storm, and other major stars. There should be a reason that the team is not the one that the MCU introduces when they bring in the X-Men. A good reason this could have happened was because of the X-Men storyline, Schism. This saw Wolverine wanting to protect the kids while Cyclops wanted to turn them into more of a military unit. Schism could have happened in the flashbacks, and the new X-Men could be the fallout with someone like Cyclops leading the young mutants in a Professor X-type role.
5) E is For Extinction

Much like the Mutant Massacre, if the MCU wanted to hit the ground running, they could use the E for Extinction storyline. Instead of the MCU having Mister Sinister send in his team to kill underground mutants, this was a bigger attack, with countless mutants murdered in a concentrated Sentinel attack. Of course, this would make mutants sympathetic to the viewers, while the people of the MCU Earth still hate them just because of how they were born. This is the least likely to happen since X-Men ’97 already did it.
4) Avengers Vs. X-Men

The first time that the X-Men appear with the Fantastic Four in Avengers: Doomsday, they will battle Captain America’s Avengers and the Thunderbolts’ version of the New Avengers. However, if the MCU wants to push this even further, there can be a full-on Avengers Vs. X-Men storyline. This could come thanks to the United States still having a love affair with the Avengers, especially if they help save the world from Doctor Doom. However, the people still need to have mutants, and this could lead to conflict between the two teams, as long as it is done right.
3) House of X

If the MCU really wants to make the X-Men different from how they were in the past, there is a good way to do so. They could start the House of X storyline by introducing the X-Men living on the island of Krakoa in their own government. This could allow the MCU to have the veteran mutants living on the island and the young X-Men fighting in the cities in America. This could also be a chance for the MCU to eventually move over in solo stories to show more of Krakoa, and the entire island nation could be a huge part of the upcoming mutant storylines.
2) The Brood

If the MCU really wants to make its X-Men different from the Fox stories, the studio could send the mutants into space. This could really give the MCU a way to show the mutants dealing with the Marvel Cosmic Universe, including bringing the Shi’ar to the MCU, especially since they have a strong connection with the X-Men via both Lilandra being Professor X’s lover and Cyclops’s dad being the leader of the Starjammers. Finally, they could fight one of Marvel’s deadliest monsters in The Brood, which could be a great group to include on the big screen.
1) God Loves, Man Kills

The best Marvel storyline that the MCU could use in its very first X-Men movie is a very personal tale with God Loves, Man Kills. This was a story about how one religious preacher named William Stryker turned the public against the mutants by painting them as demons who were there to take their place. This is a story that is still topical to this day, and one that plays into real-world prejudice and issues that take place all the time. Stryker was a military man in the Fox movies, but that is not who he is in the comics. Having this storyline of hatred, prejudice, and random murders of young mutants could be a perfect way to set up the X-Men storylines for the future.
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