Michael's need to be a white knight is what is behind his interest in Simon. He wants to know who pulled his strings and how he can stop them. He gets what he wants when he arrives at a palatial beachfront mansion where Vaughan and a vast number of armed guards have housed Simon for his meeting with Michael.
I don't know where the CIA have been hiding the dangerous rogue agent, but he hasn't been enjoying it. His face bears the marks of some rather severe beatings. Like many dangerous fictional characters it's obvious that Simon's talents go behind the physical, he achieved academically as a child before covert affairs got hold of him.
He knows he can't give information to Michael while there's a camera in the room, so he breaks his cuffs and launches himself and Michael out the window, using the little time they have to make it look convincing and at the same time tell him where he can find another piece of the puzzle.
While Michael's with Simon, Sam meets an old friend in prison. Juan has served most of his stretch and is due for release, but a prison overlord has targeted him and he doesn't believe he'll live long enough to be freed.
Michael agrees to go into prison and protect Juan, as long as Sam and Fiona go after Simon's clue, which is hidden in a cemetery. When Jesse asks Michael how he's going to get into prison, he answers that there are any number of people who would like to see him behind bars.
I actually thought he may be contacting Paxson to do it for him, but it turns out to be Lane and Harris, still paying off their favour.
Juan's tormentor is both dangerous and well connected, as well as having guards in his debt. It takes a riot and everything Michael has at his disposal to take the guy out and keep Juan alive long enough so that he can be released and rejoin his family.
Fiona finds the retrieval of Simon's package rather difficult as not only is it located in a grave in a historical cemetery with an aged, but vigilant caretaker, but it's also been sealed explosively, and will blow up anyone who tries to get it out of the crypt without knowing what they're doing. Fortunately Fiona has spent enough time working out how to blow things up that she also knows how to disarm almost anything explosive.
What's in the crypt really only brings up more questions and while Simon won't give everything away, he does tell Michael the name of the man who had his leash; a wealthy and highly successful industrialist by the name of John Barrett, who will do almost anything to get hold of Simon's encoded Bible, currently held by Michael.
There's also the revelation that Vaughan is far more involved than he ever let on from a long way back, he also knew about the burning of Jesse and in fact engineered it. A dangerous friend to have and possibly a much worse enemy.