I've been wanting to do something like this since I discovered the fan theory section of Reddit. As such, I've become a major proponent of fan theories. I find they add greater depth to a story or franchise. I also noticed that there aren't too many popular fan theories about the X-men. With that, I'd like to present one that I actually came up with after reading Marvel Legacy.
We see it happen in the X-books at least once every couple of years. Mutants are on the brink of extinction and the X-men have to save them. That was the whole plot of House of M. However, no matter what humanity tries to do to wipe them out, mutants find a way to survive and bounce back. Now, the X-men have a major role in this. That much I don't discount with this theory. However, after reading Marvel Legacy #1, I think there's something bigger at work here. It has to do with one underlying factor that drives mutation in the Marvel universe. It can be best summed up with this:
Think about it. Humanity lives in a world full of gods, aliens, and mystical forces. In nature, whenever a species faces significant stress, evolution tries to go into overdrive to adapt. We saw in Marvel Legacy #1 that gods, Celestials, and cosmic forces were on Earth as far back as a million years ago, which could have been the initial catalyst. Then, you have stories like X-men First To Last which show added influences from beings like the Evolutionaries. All these stresses could've acted as a catalyst, of sorts, to make the human genome create the X-gene. Because when you're a species in a world that's regularly influenced by gods and aliens, you need a little something more than stone tools to survive. Mutant powers could be a direct response to that.Mutants in the Marvel Universe are a direct evolutionary response to the existence of aliens, gods, and magic.
It also adds greater meaning to Tony Stark's revelation in Avengers vs. X-men. In that, he says the Phoenix Force demanded more mutants after Wanda cast her spell. Being a cosmic force, that implies that mutants were a natural evolution that need to exist for humanity to survive. In a sense, that makes the bigotry against mutants all the more important to battle because if that side wins, everyone loses. If the X-men win, though, both sides win.
I did a whole post about it on my blog, which you can read here.
Like any fan theory, I'm not claiming that this theory is canon. But I think it's one of those theories that gives an extra bit of context to mutants in the Marvel universe. I just wanted to share it with my fellow X-men fans.