I did hear a few bits of her English accent coming through every now and then. I guess she speaks like that most of the time now.

Yep - two things at the end tell us just how much of a misdirection the story was: the ship blowing up the woman, and CSM clearly being in a position of authority and worrying about Mulder and Scully.

Also, something I am surprised hasn't been mentioned by anyone else:

Correct, he was killed by essentially the new alien group that is taking over earth.

Classic X-Phile here, albeit one who had to wait a few days to watch both episodes.

I also tried "Resist Or Serve" but I got some very strange offers to clean my house naked.

Yeah it was really odd. Really wasn't Scully's voice.