Tooms is a great example of how an episode can be fucking brilliant even if it's riddled with plotholes.
First, there's Tooms himself. Last we saw him he was preparing himself a new nest. No reference to that, and indeed his psychologist doesn't even know about the nest thing and is legitimately curious when he sees him making strips of newspaper late in the episode.
Now look, I can totally see the shrink dismissing Mulder's accusations out of hand. I get that. But he should at least be aware of them. His reaction at the end of the episode shouldn't be "Oh, I didn't know you were interested in art"; it should be the slow and horrible realization that all that crazy shit Mulder was saying is actually true and this guy is about to eat his liver.
(Why Tooms is finally unable to resist the urge any longer at this moment? Plot convenience; no other reason.)
Plenty of other things like that throughout. Tooms travels through a sewer but then he hides in a closet and nobody notices the smell. The key to the mystery is a body he hid because it could prove his identity, which they ultimately do based on dental X-rays. So does he not ordinarily use his teeth when he rips people's livers out? Does he ordinarily use a knife or his fingernails or something and he just used his teeth on this guy for some unexplained reason? Was he in a hurry? If he was in a hurry, how did he manage to hide him in concrete? Were dental records even a typical crime investigation tool in the 1930's when this murder is said to have taken place? None of it makes a lick of sense.
And that he gets let out in the first place -- look, I don't care how fucking crazy Mulder's "he's 100 years old and can elongate his body" story sounds, the dude has a room full of serial killer trophies and tried to murder an FBI agent. Guys like that don't just get discharged after a few months.
I could go on -- his frameup of Mulder's pretty half-assed too, and there are any number of other false notes. But all of that? Fuck it. Because this is still a great episode. Tooms continues to be one of the greatest monsters in the entire run of X-Files. He, Mulder, Scully, and the supporting cast are all in truly fine form here. And the direction -- wonderful, creepy stuff, building toward a claustrophobic climax and brilliantly creative, satisfyingly violent resolution.
As far as mythology, this is the episode that introduces Assistant Director Walter Skinner -- essentially another government bureaucrat standing in Mulder and Scully's way and trying to shut down the X-Files, but played so ably by Mitch Pilleggi that he would later become a major character. Really, you can tell that by watching -- this guy is a one-off but Pilleggi is just so damn good that he turned into something else entirely.
And the Cigarette Smoking Man is back, hanging around Skinner's office, being sinister and not saying a word until he gets a single line at the end of the episode, Silent Bob-like. I think my favorite part is that Mulder and Scully never even acknowledge that he's there. There is no "Excuse me, but who the hell is that guy, anyway?" Hell, if you just saw this episode you could easily believe that he was a figment of Skinner's imagination.
So, in conclusion: Tooms is awesome, even if the script is really kind of a damn mess.