Whenever religion reared its head in The X-Files, I was always confused and irritated, "Revelations" being the worst offender. Somehow, Mulder, the guy who jumps to the most insane conclusions on a whim, refuses to believe in the possibility of miracles, discounting the Bible as parables. And like Scully in some of the early episodes, when evidence is presented in front of him, he balks and does what Scully does--find the typical scientific answer. In this episode particularly, Mulder comes off as a petty rebel who defies organized religion while embracing conspiracy theories for the sake of doing so.
And Mulder's absurd disbelief, in comparison to his usual blind devotion, reinforces Scully's behavior in this episode where her own lapsed faith is tested to the extreme. Her role reversal comes out of her faith--not thin air--much as Mulder's belief in the paranormal stems from his sister's abduction, and at the end of the episode, she tells a priests she hasn't confessed in 6 years.
The plot seems like a precursor to the mythology of Millennium which started the next year. There's a lot of Biblical talk and destruction, but it's a story of Scully's faith and a boy who doesn't quite know what to do. As much as the script bothers me, it's hard to look past the directing and general tone of the episode.
"War of the Coprophages"
I've watched "War of the Coprophages" several times, and it's never struck me as one of the better episodes, though many regard it as one of the best episodes of the series. Like every Darin Morgan-written episode, it's a nice balance of humor and horror, which would seem to elevate it among the pantheon of great episodes.
Upon further exploration into the episode, however, there simply isn't any substance. In between the scary scenes of cockroaches, Mulder and Scully's funny conversations over the phone, and big ideas about bugs and robots, the episode lacks a solid plot to hang on to. The episode is essentially a mash-up of the best banter of Mulder and Scully, and a few key points: aliens may regard humans as humans regard cockroaches, humans often revert to their base instincts.
The two saving graces to the episode are the cockroach scenes at the beginning and the moments between Mulder and Scully which are a pure joy to watch.