I'm revisiting the mythology episodes in light of Season 10. I know we all feel Season 10 retcons the original mythology, or at least "resets" it back to the earlier years. Keeping in mind that when the series returns, be it in the form of more episodes or in a film, what's presented in My Struggle I/II may have merely led us down this path and suddenly veer back in a direction more in line with the original mytharc, I've watched the Season 1 episodes again in light of Season 10.
IMO, nothing in "Pilot" or "Deep Throat" is contradicted in "My Struggle." I wrote a separate post on how "Deep Throat" is a very similar episode to "My Struggle," and that perhaps this is the direction CC wants to harken back to. A lot of eerie parallels between these two episodes.
"Fallen Angel" introduces more explicitly how the government deals with UFO crashes. But watching this episode, and the introduction of Max Fenig, I tried to imagine how what we see in the episode may in fact be elaborate staging. What if the UFO crash is staged? What if Deep Throat is not in fact trying to lead Mulder to the fact of alien colonization? And what if Max Fenig is used as a ploy by the government, and his abduction is merely staged? Honestly, I didn't find any of these questions too much of a stretch.
I think the fact that Mulder & Scully are led on a wild goose chase in "E.B.E." and ultimately find out they are being surveilled gives support to the idea that the government is setting up a narrative to lead Mulder & Scully toward what is set up in the finale.
And in "The Erlenmeyer Flask" we're introduced to the fact the government is experimenting with alien-human hybridization. What if the intent for these hybrids is not to withstand alien colonization, but to withstand the planned Armageddon we may be witnessing in "My Struggle II"?
Of note, here are 2 significant take-aways from the Season 1 finale, both of which are addressed in Season 10:
1. Deep Throat confirms the alien fetus Scully discovers was retrieved from the Roswell crash.
2. Deep Throat confirms smallpox inoculations contained alien DNA strands.
For Season 1, re-considering what happens, with a slant toward the possibility of there being not an alien conspiracy per se but a conspiracy fostered by the government, doesn't take that much imagination, IMO.