The starting point of the original series was that a structural engineer was going to break his death row brother out of prison by getting sent to prison himself and then using his tatoos, and his work helping the prison governor construct a matchstick model of the Taj Mahal, to tunnel out of a maximum security prison and get to Panama. Naturally, the brother was the victim of a vast conspiracy on the part of the shadowy forces controlling America, a conspiracy which boiled down to giving the vice president's brother a nice house and a set of false teeth.
So far, so not exactly cinema verite.
Some viewers have obviously felt that season 3 was stretching the plausibility of the story. This doesn't do justice to the wild implausibility of what has come before. The plot of Prison Break is total gibbering nonsense from start to finish. Season 3 is as silly as seasons 1 and 2. It's absolutely brilliant.
If you want a serious, thoughtful attempt to capture the complex, ambiguous relationship between criminal and governmental structures, watch the Wire; personally, I watch Prison Break because it's nonsense on stilts, but nonsense with a completely addictive narrative drive, played out by a fantastic set of character actors.
If you took seasons 1 and 2 for what they were - the best fun on TV - then season 3 won't disappoint you.