We know in Per Manum that Scully is 14 weeks pregnant. So, the timeline actually makes sense up to now IF she was less than a month pregnant when Mulder disappeared and IF there’s almost no time between the 11 cases that she and Doggett investigate together this season.
AND, there’s no way she could have become pregnant in En Ami with Chimera, All Things, Brand X (and Mulder’s recovery), Hollywood A.D, Fight Club (and both their recoveries), and Je Souhaite taking place in less than a month.
THEREFORE, there is no way that CSM impregnated her in En Ami (medically or otherwise), he is not the father. It does make sense timeline-wise for CSM to have known that she and Mulder were trying to get pregnant via IVF and after it failed for him to do something to her in En Ami to return her fertility. We know from season 9 that they are spying on them and knew they were sleeping together (in my current interpretation of season 7 since before En Ami).
SO she gets pregnant in Je Souhaite or thereabouts and Mulder is the father. Thank you for coming to my Ted Talk.
It’s like wake up eat breakfast look into your phone to be blasted with non stop terrible news that makes you want to die go to your job eat lunch receive more news that makes you want to die etc.
