The episode you are referring to was called Home that was banned from tv for many years after the original showing. It was also the first ever tv episode to get a TV MA rating. I have to say one of the most disturbing things ever on tv even this many years later. Hard to choose but might be their best episode ever.
Watched the 3rd and 4th episodes last night and thought they were classic X- files, enjoyed both very much. I was always a bigger fan of the Monster of the week episodes over the conspiracy ones.