Yeah they really screwed that up. The whole way they handled Scully's mysterious pregnancy was botched from the start. (I think I've written about that in different articles regarding to the mythology.) But on a personal level, I LOATHED every aspect of the storyline.
I know it was a standard of the X-Files to bring up so many major issues as storylines and then not talk about them (Scully's cancer in Season 4, anyone?) but they botched the whole thing. They basically dropped the biggest bombshell in the final minute, spent the first half of Season 8 NOT talking about it - and not even have Scully show during the first trimester. Then three months go by she's massively pregnant - Krycek says the pregnancy can't come to term and we still don't know who the father is. Then there's the shitshow of the season finale - which was another point they could have ended the series - and then the series goes into Season 9 and Scully seems to have given birth to an alien-human savior. Or maybe it was a miracle child: i ONLY WATCHED Season 9 for a rewatch for my blog (the columns aren't on Medium) and I found the whole thing distasteful.
And somehow the revival - both of them - did the impossible and made it WORSE. i haven't actually gotten around ot Season 11 (?) except for a few episodes here and there but honestly everything I saw and heard - I agree the pregnancy fixation was horrible. I'm not sur e which part was worse: Mulder and Scully finally hooking up OFF-SCREEN , the child being Mu;der and Scully's but also alien or... welll, I can't even say Option C evebn all this time later.
Scully and consent is going to happen. I'm going to be dealing with a lot of television related stuff the next few months but I will get back to it. It is always good to meet a fellow X-file fan still out there (sorry) as well as a fan of my articles. Keep looking. I've written individual pleces on many of the writers who worked for the show over its long history who were legends themselves. Two words: Darin morgan.