Jonathan Hickman’s monumental relaunch of the X-Men in 2019 with the House of X/Powers of X series has created such a massive shift in the popularity and trajectory of the mutants in Marvel Comics, that no matter what happens to Krakoa itself, mutants in the Marvel Universe will never be the same. Unless there was a cosmic rewriting of history or the mutants are fully wiped out—two things Marvel Comics will almost certainly not do—there is absolutely no way to go back to how the X-Men and mutantkind used to exist.
What makes the Krakoan Age so different from any other time in mutant history is that there is not just one single faction of mutants living on the island. Instead almost every single mutant in existence, as well as ones being resurrected, are all living together in some form of peace and collaboration. The new status quo around mutant government, developing culture, immortality, and forgiveness of past enemies has made it so that mutants and their relationship with the rest of the Marvel Universe have been indelibly changed forevermore.
Of course there is a chance that Marvel Comics could pull something in 20 or 30 years like a new Age of X-Men that rewrites current continuity, or a convoluted timeline plot that resets the mutants’ history. But Marvel has not had a fan response in years that has been as overwhelmingly positive as the reaction to the Krakoan Age. Never before in mutant history, except perhaps the time when Magneto ruled the mutant nation of Genosha, have mutants gathered in such a way, and Genosha not only ended in a mass genocide of mutants but also had much less focus than Krakoa has had since 2019. While the looming threat of this summer’s big crossover event A.X.E.: Judgement Day hangs over the mutants and threatens to destroy them, it is clear that there is absolutely no way Marvel Comics would allow the Eternals or Celestials to wipe out the mutants. The X-Men books have become so popular in the current world of comics that it would be financially disastrous for Marvel to end them.
Judgment Day might lead to the destruction of the island of Krakoa, or even somehow the ending of mutant immortality, but what matters the most is that none of these things would actually turn back the advancements mutantkind has made as a race. Gathering all living and previously dead mutants on the island of Krakoa, as well as terraforming Mars and relocating millions of once lost mutants to that newly thriving planet (an act that did NOT lead to the colonization of an indigenous people), has created a complex and beautiful culture for the mutants. In the past mutants have mainly been able to bond over the fact that they share an X-Gene, but now all mutants across Earth and Mars have a shared culture, group identity, and vision of what their present and future could and should look like. The X-Men have always been used as a metaphor for minority oppression and discrimination and for the first time in their 50+ years of existence the X-Men have moved away from Charles Xavier’s failed dream of peaceful cohabitation with humanity and instead have successfully annexed themselves from their oppressors to create a nation where they can prosper and find peace. .
Even if somehow Mister Sinister uses his clones of Moira X to reset the entire timeline of the Marvel Universe, the mutants will find a way back to each other. The X-Men’s new status quo in the Krakoan Age is so big, and has impacted so many different parts of the Marvel Universe, that there is no reasonable way that Marvel Comics can ever undo the changes that the Krakoan Age has made to the mutants.