Just reading through this thread reminds me why I was an MOTW fan, not a mytharc fan.
I preferred the monster of thenweek format, I never like the long story arcs.
I only like long story arcs when they are written intelligently, have the destination/resolution planned from the beginning, and make sense.
IOW, I don’t like long story arc shows.
…is huge waste of time and can’t even keep its own internal logic straight.
The freak-of-the-week episodes were far more satisfying.
I agree with Bryan Ekers, the show was great when it did the “monster of the week” format with occasional glimpses of the edge of a shadowy conspiracy. Once they started building the mythology, it got over complicated then started to contradict itself. For me it just has too much information to be a mysterious thing in the background, but is clearly never going to make sense or get resolved.
A question that has not been answered: Does anyone like the monster of the week episodes? 
I thought that (at least at one point) the big reveal was that there were no aliens, that the Syndicate made them up to keep Mulder from finding out their secret plan to take over the world?
I remember the moment I lost patience with the arc. There was a recurring black guy character about whom I remember very little, but at one point Mulder demanded a straight answer about something and the black guy replied “Don’t open a door you’re not prepared to go through” or something similarly vapid. It was obvious even then that Mulder had been prepared to “go through” that door since before the first episode so I felt as an audience member that my time was clearly being wasted.
But there ARE aliens. That’s a fact. At least two different species, even assuming the invasion aliens are fake.
And manufacturing a giant alien ship and burying it in Antarctica on the off chance that Mulder could actually find it and make it there (and back! which was never covered in the movie) just to provide “evidence” of the aliens is a bit far to go with the fakes.
When the Syndicate eventually does take over the world, what are they planning to do with it? 
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Maybe I’ll be the odd one, I LOVED the mytharc stuff. I enjoyed the MotW episodes of course since they were great, but it was the mytharc that got me hooked. I’m wildly disappointed that they screwed it up so badly though.
This is the structure that worked and there really was no reason for it to fall apart. They could have taken periodic trips into conspiracy land, peeling back the onion, while still successfully keeping it out on the fringe of the formulaic MotW eps. They just didn’t have a clear story. Think of it like Lost…they had no plan either and for the most part they kept finding new and mostly interesting directions to take the mystery. It all collapsed when it ended, because as noted they had no plan, yet the journey was great. X-Files could have taken us on a great journey and maybe never ended it since there’s always another cover-up.
I hated the mytharc. The only eps I care to watch are the MotW ones.
“Alex Trebek? The game show host?”
[He] didn’t say that it was Alex Trebek. It was just someone that looked incredibly like him.
Funny choice, because gdave above made a case that Jose Chung was a key mytharc episode. Maybe THE key.
Is Soft Light a mytharc episode? because it has Mr X, but otherwise no connection to the Syndicate.