The rise of Krakoa gave a sanctuary to all Mutants that sought peace from a world that hated and feared them. Now, as a sovereign nation, the Mutant species could finally earn a place in the world both as allies and a superpower. That said, where Krakoa turned enemies into allies, it also brought out the worst in many of its people, including its leaders. Characters like Erik Lensherr/Magneto completely flipped in their allegiances, going from enemy to humans to a just protector of Mutant.
However, Sins of Sinister proved that not all individuals can change their ways as Mister Sinister orchestrated a plan that was in the making for a long time. This involved seizing control of the Quiet Council and creating Sinister-inspired clones of its members, including Professor X. But as Immoral X-Men #1 (by Kieron Gillen, Paco Medina, Walden Wong, Jay Davis Ramos, and VC’s Clayton Cowles) has shown, Professor X didn’t require much of a push to be evil.
Being corrupted clones that carried Sinister’s DNA, the Quiet Council still believed in their personal dreams, but also wanted to achieve them through violent means. In the case of Emma Frost and Professor X, this meant killing anyone that threatened complete control or didn’t even consider believing in the cause. Immoral X-Men #1 saw this in action when Professor X used his abilities to compel a rebel cell led by Nick Fury to kill themselves. Though he did so without hesitation, Xavier still wept for the lives lost. But rather than cry out of guilt, he was simply saddened that they wouldn’t readily align with his evolved philosophies.
Furthermore, Xavier later mourned the loss of his friend, Magneto, who had died during the Judgment Day (by Kieron Gillen and Valerio Schiti) event, as he wished that he could see all the Quiet Council accomplished. But where a more benevolent Xavier would’ve just wished for Magneto to still be alive, this corrupted version wanted to see his friend, so he could gloat and prove that he was right and Magneto was wrong. While there’s clearly an evil streak embedded in the DNA of Xavier, past events have proven that his worst traits were only exacerbated rather than his mind being completely twisted. This was more evident when working with Emma Frost, who was a villain before a hero and was always willing to bend the rules to get her way.
While his intentions were noble, in the creation of Krakoa, this opportunity was also the first time that Mutants had a seemingly foolproof way to finally be recognized and respected. As a result, the inherent secrecy and deception that came with its creation was a necessary risk. That said, these practices had seemingly grown to change the professor, and the power he now attained didn’t help that mindset. For example, in Legion of X #9 (by Si Spurrier, Netho Diaz, Sean Parsons, Álvaro López, Java Tartaglia, and VC’s Clayton Cowles), Xavier not only took it upon himself to depower his now benevolent son Legion, but he also claimed that Krakoa was solely his island and the Mutants were his people.
Xavier’s character was also already being brought into question by those closest to him. Magneto, no stranger to dark deeds, warned Storm that Xavier’s ambition could lead to the destruction of all the Mutants in X-Men Red #7 (by Al Ewing, Stefano Caselli, Federico Blee and Protobunker’s Fer Sifuentes – Sujo, and VC’s Ariana Maher). It’s clear that the odds have already been stacked against the professor long before Sinister took control. Furthermore, he was already making morally questionable choices that were changing him as a person. In the end, while Sinister’s corruption brought out the dark side of Professor X, it was traits that likely would’ve come out on their own given more time.