WARNING: The following contains spoilers for X-Men #20 by Jonathan Hickman, Francesco Mobili, Sunny Gho, and VC's Clayton Cowles, on sale now
Since putting aside their past antagonism to help foster the growth of Krakoa, Xavier and Magneto have had to become surprisingly ruthless together. They've abandoned allies, set off conflicts with other heroes, and largely operated outside the bounds of heroic morality. They've done so while keeping their own potentially ruinous secrets, such as the continued survival of Moira X and the true reason she doesn't want any mutants with the ability to see the future to be revived.
But in their attempts to control the future of mutantkind and help ensure the survival of Krakoa, Xavier and Magneto have officially set up two major threats to attack Krakoa directly by giving Nimrod some additional motivation to hate mutants upon his activation and finally setting Mysituqe on her path for vengeance against Krakoa.
In X-Men #20, Xavier and Magneto confer with their fellow Quiet Council member, Mystique, regarding a secret mission. Discovering that the anti-mutant organization known as Orchis is still hard at work perfecting Nimrod, the shape-shifting mutant is ordered to sneak into their base via a strategically placed Krakoan Gate and sabotage the creation of the advanced Sentinel. Although Mystique is clearly disgusted that Xavier and Magneto won't take part in the attack they condone, she carries out the assault with the understanding that its completion will force them to finally revive Destiny, her long lost love -- and Moira X's greatest threat, as she believes her precognitive abilities would sew discord among the mutants of Krakoa.
The plan ends up backfiring spectacularly, with Mystique witnessing the birth of Nimrod with a human psyche (that of Erasmus Gregor, a scientist who died in the last mutant assault on Orchis). But her attempt to destroy the Nimrod fails, with the Sentinel overtaxing itself to counteract her bomb. Erasmus's psyche is effectively erased in the process -- breaking the heart of Nimrod's inventor and Erasmus's widow Alia. This leaves Nimrod with an even greater hatred for mutants, setting up the Sentinel to be even more aggressive in the inevitable conflict between Orchis and Krakoa. In essence, the sneak attack from Krakoa may have just set up Nimrod to become the ultimate threat to mutants, as seen in alternate realities.
Revived back on Krakoa following her death at the hands of Nimrod, Mystique demands that Xavier and Magneto fulfill their side of the deal despite her defeat. But rather than revive Destiny, they refuse -- as they've done numerous times before. They even dismiss Mystique in the process, enraging her. Seemingly unbeknownst to them, Destiny had predicted Krakoa and the machinations of Xavier and Magneto preventing her revival. She made sure to warn Mystique of this possibility and made her wife promise to destroy their island nation if it came to pass. Mystique has already been considering taking action against the island, but it appears that this may have been one last attempt to avoid catastrophe by the shape-shifter -- only for Xavier and Magneto finally angering her enough to turn on Krakoa.
The X-Men and their allies have been dealing with numerous threats since the formation of Krakoa, trying to overcome the seemingly endless enemies that the mutant nation has racked up in its short time of existence. Enraging those enemies will only make matters worse, and could lead to some unexpected union of the enemies of Krakoa -- and the possible end of the last great hope for a mutant homeland.