That sounds slightly familiar, but only just. If it's a third season ep, I only made it through about the first month or so before I gave it up as a bad job. (This is the same impulse that kept me from commiting to Fringe, the suspicion that the show runners don't really know what they're doing and they're going to jerk me around for the duration.)

Mind you, I do have vague memories of Scully getting abducted...