Was this major X-Files plot twist planned all along?

Question

The X-Files Season 11 is currently airing on television. The first episode, "My Struggle III", featured the following major plot twist:

The Cigarette-Smoking Man reveals to Skinner that Mulder is not the father of Scully's son William. In fact, the Smoking Man is William's father.

He further explains that

he impregnated Scully (unbeknownst to her) using "alien science"

while the two were alone on a trip in the Season 7 episode "En Ami".

This provides a new explanation for

Scully's ability to conceive despite having been declared barren due to the effects of her alien abduction in Season 2.

To me, "En Ami" always felt a little out of place: its plot was related at least superficially to the "mytharc" but it seemed to be more of a standalone episode. Also, the odd scene where

Scully wakes up without her clothes in the Smoking Man's chalet

was never revisited (until now).

Note also that "En Ami" was the 15th episode of Season 7, while "All Things", in which we see the first suggestion that Scully and Mulder might have a romantic relationship, was the 17th episode. It thus seems possible that

"En Ami" was purposefully situated at a point in the season that would coincide with the timing of William's conception.

Was the recent plot twist planned as early as Season 7 or is it a purely new invention by the creative staff?

Answer 1

The answer is "ISH"

According to X-Files creator Chris Carter:

I'd always imagined revisiting it. I'd been thinking about it since Season 7. Parentage was something that I had wanted to have a question mark around it. That incident in that episode, I knew we would revisit since it was such a remarkable episode in that Scully was momentarily in league with Cigarette-Smoking Man. So it was sweet for me to be able to connect that dot from so long ago.

I think maybe it was an idea he'd toyed with in the past, and finally had an opportunity to bring it back around:

I think it makes total sense. The Cigarette-Smoking Man has affected Scully's life in so many ways and not the first time her physical body. Originally there was an implant and there was an abduction and Scully's actually been abducted, if you count them up, abducted eight times in this series. So he has been involved intimately in her life. This, though, is the greatest intrusion that we've ever told.

Chris Carter Interview