Marvel comics Editor in Chief Axel Alonso recently dropped some hints as to the fate of the X-Men in a new post Secret Wars Universe at CBR. Minor Spoilers if you haven't been reading the lead up events to Secret Wars.
Here is his full answer to what is happening to the X-Franchise past this summer:
The X-Men office is taking the opportunity of "Secret Wars" to build an entire new world for the characters — to create a shared universe within the X-books that's set off by a huge event/incident/surprise. At that point, they're going to introduce a new team that feels unlike anything you've seen before. It'll be... "extraordinary."
Well first off I wouldn't be surprised if one of the new X-men books is called the Extraordinary X-men. But more interesting is that there has been rumors of the X-men splitting off into their own universe without the rest of the Marvel heroes we know. Furthering this speculation is another answer he gave with regards to Uncanny Inhumans the new Inhuman book launching soon:
"Uncanny Inhumans" allows us to explore the divide between the Marvel Universe-proper heroes and the Inhumans, and see the extent to which it can be bridged. The Inhumans have emerged as a power-player in the Marvel Universe. In coming years, we will see if it's big enough for humans, mutants and Inhumans.
This conflict that is coming between Inhumans and mutants seems inevitable as both species are experiencing a resurgence in population. The mutants thanks to the events of AVX and Inhumans thanks to the events in Infinity.
But how would the X-men get their own world or even universe? Well so far leading up to Secret Wars we really don't know anything about the state of mutants other than they are once again unified and led by Cyclops in a place now called Nation X protected by sentinals. And Scott has a Phoenix Egg. That whole situation is interesting considering that in the comics that are behind the "Time Runs Out" event, Scott is still considered a criminal and Storm and Beast are leading the Jean Grey School for mutants after Wolverine's death, and there is still a time displaced X-Men team running around.
Furthermore, it has been shown that the Beyonders (the supposed group behind the destruction of the Marvel Multiverse) have been killing off all cosmic entities across the Multiverse, even the Living Tribunal. But they were not shown killing off any of the Phoenixs present across the universes. Which means either the Phoenix and the Scott's mutant nation play a big role in Secret Wars, or they use the egg as the way to split them off after Secret Wars ends. Or maybe even the egg is used in the creation of Battleworld. Whatever the case, it will be interesting to see a Mutant only world if it does happen.
Rick Remender played with this idea in the first Uncanny Avengers run, and the world looked cool full of interesting stories to tell.
Or this could all be a smokescreen and Axel was just speaking in metaphors to get Marvel fans speculating like crazy.
Top image "Uncanny X-Men" #600 cover by Chris Bachalo.