The Feds make a lot of promises in exchange for testimony, not all of them moral, and it's the Marshals who are stuck with the consequences. This is possibly Mary's least favorite part of the job. She's got enough problems with the witnesses who deserve her protection.
When New York City art dealer Jay Arnstein goes into the Witness Protection Program, he asks that his wife, Marci, be moved with him. Typically, this wouldn't be an unusual request but in this case, it was Marci who ratted out Jay to the FBI for his illegal art dealings. But Marci is looking as entering WITSEC as a chance to start over-an optimistic attitude if there ever was one. But what has really stuck in Mary's craw is that Jay made a separate deal with the Department of Justice to bring along his mistress, Kay, for the ride. On top of that, the rules of the Program force Mary to keep this detail from Marci, a very sweet woman of whom she has grown quite fond (a rare yet occasional occurrence).
Things might have gone on like that forever-until Kay shows up at Jay's new gallery opening, sending Marci into a bit of a tailspin, since she was under the impression that she and Jay had rekindled their romance making their marriage better than ever. This would've been a mess for Jay to deal with-his idea for which is to break up with Kay and have Mary ship her off to another location-but when he is shot later that night, it becomes Mary's responsibility to clean up.
Mary's also got a bit of a complicated situation on the home front herself: Raphael has torn his ACL and is not only back home from Florida, but on Mary's couch recuperating until the swelling goes down and he can be more mobile. But instead of Mary becoming Raph's nursemaid, it's Brandi who takes on the Florence Nightingale role-though it's unclear who is more surprised by that particular development.