Factual error: Mulder refers to a Royal Navy vessel that sailed from Leeds. No large ship can sail from there - it is at least 50 miles from the coast.
Deep Throat - S1-E2
Mulder: They're here, aren't they?
Deep Throat: Mr Mulder, they've been here for a long, long time. (00:49:58)
Trivia: The Cancer Man smokes Morley cigarettes, a fake brand that has appeared in a number of TV shows and movies since the '60s.
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Answer: SPOILER ALERT: Hook up, yes. Married, no. Children, maybe. The rumors that Mulder and Scully were married started when David Duchovny (Mulder) called Scully "Mulder's wife" when discussing the return of "The X-Files" show. However, series creator Chris Carter said "they were together but never married." In the 2nd X-Files film, "I Want to Believe", they are in a romantic relationship. But by Season 10, they are broken up as Scully has left Mulder. It is revealed that Scully's son, William, is the son of The Smoking Man, who is Mulder's father as well. In Season 11, Mulder and Scully hook up again and in the last episode of Season 11, Scully tells Mulder she's pregnant with his child. As of now, there are no plans for a Season 12 and Gillian Anderson (Scully) has no intention of returning to her role in "The X-Files."
Bishop73
I want to add, it's possible that they live together as partners and are legally common-law spouses. Or they consider each other to be "husband and wife" in a spiritual/sentimental way. I've known or heard of a few couples who did that. For whatever reasons, they did not want a legal marriage with documentation. But, for now, this is just fan speculation. Gillian Anderson and other cast members might change their minds someday.