The writers of Prison Break said that they have already planned for only 2 seasons. With season 1 being in prison, and season 2 being out of prison, after which all wrong is corrected.
However, given the show's success, they decided to change elements in the 2nd half of season 2 to pave way for season 3.
It's easy to imagine how the original season 2 would have ended, from what actually was shown.
Lincoln and Sara exonnerated.
Micheal's initial sentence removed (as the judge in the Series Pilot was inclined to, before Scofield's "no contest" plea), with the help of the Governer's friend.
Kim killed, and Mahone runs away.
However, the writers changed very few details that gave a way for Season 3 to happen. Sona was not mentioned at all in the 1st half of season 2. It changed everything and gave way for a brand new story.
Now those last 5 mins in season 2 looked like a scene from Waterworld. I mean are there no courts in Panama? No legal system? Of course there is.
A man shot another one in self-defense on gunpoint. Kim's body along with Kim's gun are in the sea. Are there no grounds at all for a non-guilty plea? Or at least a lightened sentence? But not 1st degree murder.
What about Mahone (charged for drug-trafficing) being thrown in the same jail as Micheal?
Now finally, the "General" at the all-white research facility. Is Season 3 going sci-fi? What's that talk about "We want him to break out". Are they conducting some sort of psychological research, or some "prison-improvement" facility? They couldn't have meant they want him out so they can kill him. Because getting killed in this place is the easiest thing to make happen. That "bigger military sci-fi plan" look left me uneasy.
Micheal summed it all when he said "My brother's been exonerated, the President stepped down. We're not a threat anymore." This is what it's all about.
Breaking out of any other prison, be it Sona, will never be as charismatic or nearly as good as Fox River. Because there is no plan. No tattoo. Nothing. That was what made Season 1 amazing.
That talk at the New York military research facility looked so much out of this show. It was not like PB at all. I hope Season 3's pilot would be as strong as season 1's pilot, because this is a brand new story they're starting.
An interesting theory is that there may be someone in Sona who is important for the company, and they want Micheal in there to break him out. Which is actually not that good because Micheal's company designed Fox River, not every prison on the planet. Well I guess it's theory time till August.