Yeah it just got too redundant. Every time they finally “revealed” the big plot of the secret masters it turned out there were other even more secret masters with a bigger plot. After 3 of those reveals I just got tired of it, I watched about half of the season after the movie and that was it, highly unlikely I’ll watch the second movie. I’ve moved on from the X-Files.
I got bored with the UFO aspect almost from the start, lost track of the conspiracy, and quit watching those episodes. I really enjoyed almost all the episodes that didn’t deal with aliens though. It was like two separate shows.