The following contains spoilers for A.X.E.: Judgment Day #3, now on sale from Marvel Comics
The X-Men have always been prone to in-fighting, but the era of Krakoa has strained the mutants' ties to one another like never before. While the period after Krakoa's founding was initially one of unity, the pressures of running a nation full of powerful and ambitious mutants have taken their toll. The most recent issues of the various X-Men series have shown that internal conflict is spreading to every corner of the island.
In A.X.E.: Judgment Day #3 (by Kieron Gillen, Valerio Schiti, Marte Gracia, and VC's Clayton Cowles), the Quiet Council made a dangerous decision that put millions of lives in jeopardy. It creates an irreconcilable rift between them and the X-Men that could plunge the mutant nation into an all-out civil war.
The re-animation of the Celestial Progenitor brought the destructive war between the X-Men and the Eternals to a decisive end. However, the conflict is far from over -- the newborn god's subsequent announcement that the inhabitants of Earth had just 24 hours to justify their continued existence or face extinction drove Krakoa's Quiet Council to take drastic action. Over the objections of Kitty Pryde, Colossus and Nightcrawler, the Quiet Council sent the X-Men to kill the Progenitor by destroying one of the nodes holding its body together, withholding the fact that the attack could trigger an explosion that would kill millions.
While the X-Men seemingly went through with their mission and condemned most of the Earth's population to a fiery death, the Progenitor saw the attack coming and prevented it by creating an illusion that showed the world what would have happened if it had succeeded. Unfortunately, this also exposed the Quiet Council's willingness to sacrifice innumerable humans to save Krakoa to the assembled heroes. Among them were the X-Men, who were distraught over their role in what could have been a global massacre.
Although the Quiet Council only acted after Destiny asserted that the odds of the Progenitor's death causing an extinction event were slim, it's unlikely that they would have done anything differently if the chances had been higher. From the moment the Quiet Council held its first session, it was clear that the governing body of Krakoa's top priority would be ensuring that their newly-formed nation would prosper by any means necessary. While this mentality helped transform Krakoa into a political juggernaut, the Quiet Council's recent decisions have demonstrated an unsettling willingness to cross moral boundaries to expand their nation's influence and silence internal dissent.
Unfortunately for the Quiet Council, their descent into authoritarianism has driven a deep wedge between them and many Krakoans, particularly the X-Men. Unlike most of Krakoa's other mutant teams, the X-Men have remained committed to defending both mutants and humans. Their refusal to accept the Quiet Council's iron-fisted and secretive nature has slowly soured their relationship. Now that the X-men are aware that the Quiet Council ordered them to carry out a mission that could have ended with millions of innocent people dying, the team's faith in Krakoa's governing body could deteriorate completely.
If the X-Men and the Quiet Council do come to blows, the resulting conflict would undoubtedly split Krakoa's mutant society down the middle. While the members of the X-Men aren't the only mutants who have expressed dissatisfaction with the council's heavy-handed rule, none of them have been willing to challenge their nation's governing body. However, if the X-Men do openly rebel, other more open-minded mutant factions like the New Mutants and Nightcrawler's Legion would likely lend their support.
Regardless of who the X-Man have on their side, taking down the Quiet Council won't be easy as it's more than equipped to face off against them and any allies they can muster. Not only does the council have omega-level mutants like Exodus among their ranks, but factions like Storm's Brotherhood of Mutants and Beast's X-Force would almost certainly side with the governing body of the nation they've dedicated their lives to serving. With so much power at each side's disposal, it's impossible to judge who would emerge victorious in this hypothetical war.
An all-out mutant civil war would be a game-changer for the X-Men's current status quo. Destiny's precognitive ability has already confirmed that Judgement Day will prove to be a turning point in Krakoa's history and that the current age of Krakoa is about to end one way or another. While it's currently uncertain who or what will usher the next chapter of mutant history -- a war between Krakoa's mutants is the most likely candidate.