Ok, I've been reading up on Wikipedia. Here is what I've gathered:
Michael's brother Lincoln was framed for the assassination of the Vice-President (now President)'s brother who is in reality alive. She may or may not have also assassinated the President.
They framed Lincoln because Lincoln and Michael's father knew too much about Ecofield's dealings with "The Company" (who from what I gather is more or less the Illuminati). The father is working for an anti-"The Company" group.
Michael managed to break out Lincoln and 8 other convicts and they are on the run trying to get to Utah to recover Westmoreland's money and then leave the country. However, they are being chased by Special Agent Mahone, who was recently shot by the President's body guard Kellerman who wants to help Michael and Lincoln.
Does that about sum it up?