_Gillian Anderson (I)_ had already an advanced pregnancy in these episodes. Because of this all her shots from this episode to The X-Files: One Breath (1994) are done in a way that her belly is not shown.
If you look closely at the papers that both Mulder and Scully print out with the "contact" information on them, one column reads "10.13" over and over again. "10-13" is the name of Chris Carter's production company as well as his birthday (October 13, 1956).
This episode features the first visualization of Samantha's abduction. It differs from the way that Mulder talks about it in The X-Files: Pilot (1993) and The X-Files: Conduit (1993) but Chris Carter has said that this is down to Mulder's shaky remembrance of a hugely traumatic event.
At about 13:10 into the episode, Senator Matheson tells Mulder that "... in the next 4.5 million years, when the sun exhausts its fuel and swells to engulf the earth..." Is a mistake in scientific principle; one having nothing to do with the other. While it's most likely that life will end on the earth in approximately 4.5 billion years from now because of the heat being flung off in effort to use more dense materials to burn, it will no longer burn effectively, but the earth will not be engulfed for almost double that amount of time; an additional 7.5 to 8 million years from the time that life is no longer able to survive on the surface. Thus, what he's telling Mulder is both true and false.
Not surprisingly, Mulder's computer password is "trustno1". These were the last words that Deep Throat said before he died, and was indeed used in the titles of the season 1 finale, The X-Files: The Erlenmeyer Flask (1994). "Trust No 1" would also be the title of an episode in Season 9.