So the first "chapter" of my story takes place in a prison. I'm thinking the first chapter takes place 2-3 years before the rest of the story (along with training MC's bro just to get it out of the way). My MC gets life in prison for armed bank robbery. In those few years, our hero slowly gathers up the resources and skills needed to become a much better criminal. At the end of that chapter, the hero escapes with his friend disguised as a CO. Together they set out on a journey as fugitives to escape a corrupt nation that has brought nothing positive to their lives. In this setting, I'd hate to write a "main villain" for that one chapter then to throw him away and act like he never existed. I want my main villain to start off as the head warden of that prison. Then when the hero escapes, he rises through the ranks (he is in the military) and becomes a high ranking general. A leader of a task force dedicated to hunting down fugitives. And they have their sights set on the hero. I want this to be realistic. Sure my fictional dystopian country set on a different planet and in the year 2150. But I want this nation to both slightly resemble US policy (since that's what I know), but also be really smart because they learned from the mistakes of every other nation that has come before them. Or I could also have them not wait as long and just get on with the escape plan, since it's not mainly about prison.
Military officers usually get a broad range of assignments on their path up the rank hierarchy, giving them experience in a variety of different areas. As a reader of military fiction myself (not someone who has been a part of a military) I would find it plausible for an officer to be assigned to command a military prison for a while, while serving other assignments before and after that could have little to do with incarceration. The assignments may be in complementary areas though. If it is a large prison, they could be a brigidier already, or perhaps a Colonel. You could research the current commanding officers of prisons such as Fort Leavenworth and Guantanamo Bay to think of two off the top of my head (used for soldiers who commit crimes and for enemy combatants respectively). Their careers may be public record. In general, military bases are commanded by higher ranking officers, and there may be a broader command structure that you could use, such as the commander of the base that the prison is on. For other non-Warden positions that may still be involved, I can think of plenty of officer bad guys in movies too who had kind of floating "fixer" assignments, where they would go in and address various problems for their superiors. Like Stryker from X-Men maybe, or on the totalitarian side, the bad guy from Raiders of the Lost Arc.
