The following contains spoilers for A.X.E.: Judgment Day #3, now on sale from Marvel Comics
The Eternals and X-Men conflict at the center of Judgment Day has been on a monumental scale, with the entire world upended by the battle. All of this chaos is predicated on a surprising discovery that the mutant nation just inadvertently confirmed.
A.X.E.: Judgment Day #3 (by Kieron Gillen, Valerio Schiti, Marte Gracia, and VC's Clayton Cowles) seemingly confirms the Eternals' recent discovery that mutants and the Eternals' enemies known as the Deviants do indeed share a common genome. This means the two species might also share enemies going forward.
At the heart of Judgement Day has been the discovery made by Druig upon his ascension to the role of Eternal-Prime. After having discovered an apparent tie between mutants and Deviants on a genetic level, Druig expanded the Eternals directive to eliminate Deviants to also target mutants. Upon his failure to destroy Krakoa directly, his aggression has taken a more direct form, with armies of Eternals weapons (and even the fearsome Uranos) being unleashed against the mutant nation. Throughout, the mutants have resisted the designation that they are Deviants, but that point seems to have been countered.
As the mutants try to find a way to counter the Eternal's attack and struggle to contend with the massive Hex that are attacking Krakoa, Cyclops is shocked by a surprising alliance made by Emma Frost. It turns out that in secret, Emma has been making diplomatic overtures ot the Deviants, who rally to the mutants defense. Despite Cyclops' declaration that mutants aren't Deviants, it turns out they share enough genetic material that the Deviants can easily pass through Krakoan Gates, which is a big deal.
The Gates are specifically designed to only allow mutants and select humans pass through, and even the humans have to be cleared. For the Deviants to simply step through the Krakoan Gates suggests that at least on some level, they are indeed mutants or rather, mutants could truly be argued to be Deviants.
Although this had already been set up, it's worth noting how important this really is. Now that mutants and Deviants are confirmed to share some common genetic history, both communities are tied together on a lot of levels. If the ancient citizens of Arakko (or rather, the survivors of Arakko at this point) can be considered mutants, why can't the deviants? This could turn the Deviant city of Lemuria into a dedicated ally to Krakoa, and a place where the mutant heroes could retreat if things take a desperate turn for them.
But it also means that the mutants and Deviants might formally gain the attention of the respective communities' foes. For the Deviants, this means the forces of Orchis and the potential Sentinel armies commanded by Nimrod could determine their species is a viable target. Meanwhile, the Eternal's directive to destroy Deviants might drive them to carry on their persecution of mutants long after the events of Judgment Day. In effect, this revelation could set up a scenario where the X-Men and the Eternals are always at war. If they're lucky, the Celestial born from Iron Man, Mister Sinister, and the Eternals will be able to overwrite that directive otherwise, the endless cosmic race might find themselves in a forever war with the immortal mutant nation.