(spoilers)
I could be wrong but I believe it's Scully that breaks down and village/cult are worshipping this wierd slug like creature that burrows into peoples backs and attaches itself to their spine eventually killing them. The creature turned out to have some kind of mind control over the people of the village.
That was actually very late in the show during a time Mulder had went missing for several episodes and Scully working with agent Doggett who was played by the guy that played the t-1000 in terminator 2.(can't remember his real name)