In 2019, Professor Xavier declared mutant sovereignty on the island-nation of Krakoa at the onset of the Dawn of X era. All mutants are welcome to live in this new nation, with portals that lead directly to it accessible from all over the world. In doing so, the X-Men have become a new world power. In fact, they now stand apart from the rest of humanity -- which made lead to a new conflict with the Avengers.
In order to achieve their new status, the mutants leveraged a miracle drug that cures all manner of human diseases. This drug is available to any country who recognizes their sovereignty. Heroic and villainous mutants have finally banded together like never before, a union that has altered the power dynamics of the entire world.
The problem is, this new position has started to change them. Now, the mutants are starting to act more like villains than outright heroes, as they choose to look out for their own kind and no one else. Even Professor X himself has made it clear he plans on ruling over mankind. With this massive dynamic shift and this darker turn for the X-Men, it might not be long until they attract the attention of the Avengers. If that happens, then it's possible the Marvel Universe may be gearing up for another Avengers vs. X-Men war.
Ever since the X-Men declared mutant sovereignty, their relationships with fellow heroes have started to change. In fact, in the currently-unfolding X-Men/Fantastic Four miniseries, the two titular super-teams have recently gone at war with one another over the fate of Franklin Richards.
Franklin is the son of Reed Richards and Sue Storm and a member of the Fantastic Four family. Uunlike his parents, he is a mutant. The X-Men have tried to recruit him to come live on Krakoa to help fix his powers, but his parents want him to stay home. It hasn't helped matters that the X-Men now live with Apocalypse, Mister Sinister and nearly all of their worst mutant enemies, who sit on the Quiet Council of Krakoa. To Sue Storm, the X-Men aren't even heroes anymore.
Plus, it's not just the Fantastic Four. In the pages of X-Men, it was also revealed that the mutants still have an ax to grind with Wanda Maximoff, aka the Scarlet Witch. Wanda was responsible for the near-extinction of all mutants, something the race of super-powered beings has finally overcome in recent years. Still, the damage she once did is considered a massive offense against mutantkind and many still see Wanda as a monster. If they ever come face-to-face with her, there's no telling what could happen next. Since Wanda is closely associate with the Avengers, this could lead to a conflict.
What's more, the X-Men also have a potential ally out there -- a mutant who has yet to join their nation and who is already at odds with the Avengers: Namor, the Sub-Mariner. In the pages of Avengers, a conflict between Namor and the eponymous team has been brewing and it just got potentially much worse. In fact, through the manipulations of Mephisto, Namor has been convinced to seek out the Phoenix and harness its power against Earth's Mightiest Heroes.
For the time being, there are no connections between the two storylines, but given that the X-Men are rallying all mutants to Krakoa and Professor Xavier has already sought out Namor, they could eventually become allies. If that happens, then all-out war could break loose.
This could potentially setup a sequel to the Avengers vs. X-Men storyline from 2012, which saw the the two titular super-teams come into conflict over the return of the Phoenix Force on Earth. Since the Phoenix was the cause of the first event and since it's now set to return alongside Namor and, by extension, the mutants, the cosmic force could become the source of another confrontation between the Children of the Atom and Earth's Mightiest Heroes.