OK, so I figured out how Prison Break is going to finish
Well, here's my take:
Michael and the gang are now trying to get back at the Company for 2 reasons:
2. Some sort of attempt to clear their name although it's very unclear in the current situation what they are being cleared of - Linc was already exonerated, Sarah was never really accused of anything in the US, Michael would probably take the rest of his 5 years sentence without having to break out of Fox River as a welcome break and Sucre...well seriously, who cares? And Alex also seems to have disappeared - I'm sure now he's killed Wyatt he just wants to settle down to peace, quiet and pharmaceuticals.
In addition, it looks like Michael, who is the genius (in the old sense) of the show is obviously dying due to
So what's next? I think it's clear that the Company is the cockroach of all conspiracies - no matter who Michael and the gang team up or make a deal with, someone else will turn up and overrule or shoot them. It's possible there will be more flailing around until they realize this - Michael and Linc might erroneously think targeting the General is the answer to their problem, but while it might be cool to see him taken down, someone else will certainly grab the Company's reins and keep riding roughshod over the guys.
Michael will discover that the conspiracy is even deeper than was supposed (isn't it always?) and find his family has been genetically manipulated for generations by the Company to produce a criminal mastermind they can use for their nefarious purposes. In addition to super intelligence and insane paranoia, it turns out that Michael also has psychic powers that allow him insight into things happening at a distance. The experiment was also supposed to make him super strong and impossible to kill, but Linc got all those genes.
As the deterioration of Michael's condition continues, the Company is beginning to despair of making good on their centuries-long investment. Linc and LJ clearly don't have enough of the sneaky/smart genes to be a viable bloodline, so after more double crosses involving Scylla (another red herring) the brothers are captured and subjected to a freakish experiment in the Lab deep underground at Company headquarters. In this experiment, Michael's brain is transferred into Linc's head (in the process leaving him colour blind). To ease the psychic trauma, Michael's mind is carefully blanked - leaving his talents intact but depriving him of any memories of his former life.
Michael (now in Linc's body) wakes up naked on an island close to Seattle...