In season one Michael goes to prison on purpose to break his brother out of jail, because he was convicted of a crime he didn't commit. Michael made a few attempts to escape and at the very end of the season they narrowly escaped without being caught. 

Michael gets caught and Panama and goes to a jail called Sona. In that prison also is a man from the company and Michael now has to break this man out. He gets a little bit of outside help from his brother and at the end of the season he also barely escapes without getting caught.

After Michael escapes Sona he still has to go to jail in the US. But a person in the company that is trying to take it down hires Michael and a few other people so they can take it down. In order to do this they need to collect this device Syla. Syla has five different locations and they have to get very creative on how they collect the device. 

After Michael was presumed dead he has resurfaced in Ogygia in Yemen.  Old friend's from prison Lincoln Burrows and C-note try to break Michael out of jail, while back in the US Michaels wife is being hunted by the company in a operation.