Legion pulled a fast one on its audience, as it slowly built to the revelation that David Haller - Charles Xavier's biological son - is the villain of his own story.
David crossed the point of no return in the season 2 finale when he altered the memory of his girlfriend, fellow mutant Syd Barrett, removing any remembrance of their relationship problems, then slept with her. Rather than take responsibility for his transgressions, David abandoned Division 3 and began a cult; he would eventually recruit Switch, a mutant time traveller, in an attempt to rewrite the past and restore what he perceives to be the proper timeline, where he and Syd are still in love and he's still the hero.
How could the offspring of the most iconically benevolent mutant become such a delusional monster? The answer begins in David's infancy, when Amahl Farouk - the powerful mutant telepath known as the Shadow King - had a confrontation with Xavier, which he would ultimately lose. Assumed dead, his consciousness survived and attached itself to Xavier's infant son - destined to be a powerful mutant in his own right - as revenge. We don't yet know the exact details of David's earliest days possessed by the Shadow King, but he would eventually be given up for adoption by either one or both of us his parents and endured a difficult life, with his unhinged mutant abilities and constant torture at the hands of the malevolent entity being treated as a serious mental illness for most of his life.
David would eventually free himself of Farouk with the help of Melanie Bird and her team of mutants, including Syd, who switches bodies with anyone she touches. David and Syd had an unusual but sweet romance that blossomed as David attempted to shake the Shadow King. But David - in control of his own mind for the first time in his life - had somehow changed. The broken but charming man was slowly replaced by an arrogant, self-serving hypocrite who wielded almost unimaginable power in increasingly troubling ways. Rather than feeling thankful that he was finally free, David framed himself as a perpetual victim, justifying any action by virtue of the universe owing him for his troubled life. Assaulting Syd was the moment he made the final step from amorality to open criminality, and he has no interest in apologizing for it.
This is thorny philosophical territory for Legion, a show ostensibly about superheroes. It's impossible to know if David was irreparably damaged by sharing a mind with the Shadow King for so many years, if he was already susceptible to mental illness, or if on some level he was always going to end up as a toxic creep. For David the answer is clear - this is all Farouk's fault, and the world is unfairly judging him, the true victim. That mentality - along with a ruthless time travel scheme - could lead David to take the kind of lethal actions he's been reluctant to so far.
We know Xavier will finally debut on Legion this season - played by Game of Thrones and Counterpart star Harry Lloyd - and given Lloyd's age and the nature of David's plan, it will likely be in flashback. Whether Professor X makes a proper present-day appearance is still an open question, but one thing is for sure - he'd be horrified to see what's become of his son.