Before I write one of these posts I usually look round online to get a feel of what everyone else is saying about it, mainly because I like to say something different. That exercise of looking around can often be quite informative, and in this case an awful lot of what is on the Internet is purely descriptive. And appreciative, because I don't want to imply that this episode is rubbish when I start criticising it...
...which will start now. The reason the commentary on this episode is descriptive is because you need a commentary to keep up on everything happening. It's a bit difficult to think of parts of the X-Files mythology which don't get a mention, but I suspect Samantha escapes without being brought into this. Otherwise it's a riot of aliens, conspiracies, and shifty characters, ending in the X-Files getting shut down, which can really come as a surprise to no-one.
I particularly like Scully's role in this, in addition to being the mystified scientist she really goes out on a limb after discovering that the substance Mulder gets her to have tested shouldn't exist, by stealing an alien. Like you do.
As always, writing about TV programmes illuminates them and after all these years I am rather embarrassed to find that Deep Throat is based on a real person(and also to be reminded of the reason his name always sounds like a sex act to me):
The perfect period and identity for an informer in this show.
So to conclude: way too much going on, but one of the all time great episodes of the X-files.