"They", the company probably want Michael work for them considering how freaking smart he is. They are thinking he is the next replacement for Mahone.
I didn't think there was a killer cliffhanger left for us but it did leave you thinking about season 3 already. I mean we have Michael, Brad, T-Bag, and Mahone all in the same prison in Panama with Sucre, Sarah, and Lincoln to get them out. Roles have now been reversed and Michael and Mahone are most likely going to have to work together in order to get out. Don't forget Bellick probably has to be a part of the plan since he is the only person who knows where MaryCruz is locked up.
All charges against Lincoln were dropped due to the confession of Kellerman but Michael, T-Bag, Sucre, C-Note, and the rest didn't get charges against them dropped (but yes, I know C-Note made a deal with the fed when he told on Mahone). I'm sure that Michael's crimes will also be dismissed since he only went in prison to get his brother out of prison but the rest of the guys were in Foxriver Pen. for a reason. The cops have to totally be after them still so it should be interesting to watch an on the run criminal try to break his friends out of prison.
Oh, why was T-bag able to use his hand that Michael shoved something through? I was really looking forward to seeing him have no hands at all.