The list of victims that Scully reads from Skyland Mountain is actually a list of members of the cast and crew of the show.
At the end of the opening credits, the screen that typically says "The Truth Is Out There" instead reads "Resist or Serve."
The boy who acts as the messenger at the beginning of the episode is the son of series producer Joseph Patrick Finn.
The site where Cassandra Spender, Scully, and the others converge is said to be Ruskin Dam in southeastern Pennsylvania. There is no Ruskin Dam in southeastern Pennsylvania (or any other part of the state, for that matter), but there is one in British Columbia, Canada, which (not coincidentally) is where the X-Files was filmed at the time the episode was made.
The title of this episode is taken from a song title by Blue Öyster Cult from the album Tyranny & Mutation. Incidentally, BOC has written a few songs about aliens and the Men in Black.