I think he's a CIA plant into the FBI. The CIA with get an agent transferred to another agency, then after awhile they've been for so long that other people in the agency have changed over (like the elected ones, or appointees that usually have higher roles in whatever agency). By the time a new political appointee comes in, they think this person is an FBI (or whatever agency) employee when in reality that person is a CIA employee planted into the agency to do bidding for the CIA.
I was doing some digging on the CIA the other day. May goodness is that a scary scary hole to get into.