The comicbook story thus far has been that the Celestials experimented on mankind to help unlock their potential, which inevitably spawned mutants across time. The Celestials have yet to play a large role in the MCU outside of Ego, who we saw in The Guardians of the Galaxy Vol 2. It was said that Ego was the last of these extraordinary beings, but it wouldn’t take much to bring them “out of hiding” from the furthest reach of the universe to help with storytelling if the Disney/Fox deal goes through according to plan.
Interestingly enough, in the original source material, the Celestials were also credited with creating two other beings known as the Deviants and Eternals. Kevin Feige and the team over at Marvel Studios have been in talks of eventually developing a movie centered on the Eternals, which could also help introduce mutants hand in hand if that’s where they are going with things.
Maybe it’s a bacteria that was introduced into the human gene pool which ultimately sparked the mutation that we are hoping to see in the MCU?
In any case, keep your eyes peeled for more theories on how things could all line up for the best, and be sure to grab a copy of the Astonishing X-Men #13 at a local comicbook store near you!