Alex Mahone had one of the most dramatic changes of all of Prison Break‘s characters, yet William Finchter’s villain was not in season 5. Prison Break might have begun on a relatively small scale, with most of the main characters in Prison Break just trying to escape from Fox River Penitentiary. That said, as the show went on, Prison Break‘s story expanded to include an escape from a different prison and a government conspiracy that had overtaken the prison theme by season 4. By then, some of Prison Break‘s main characters had switched sides, including Michael and Lincoln’s former nemesis, Alex Mahone.

https://screenrant.com/prison-break-season-5-alex-mahone-william-fichtner-missing-why-explainer/