
Great episode. Well done, all around; great story that for once, feels fully realized. So many episodes up to this point feel like good ideas, and they don't always get off the ground, or come to a natural end, or get fleshed out entirely without feeling rushed. If EBE were a movie, you wouldn't walk out of the theatre disappointed.
Do you know what makes this episode really excellent?
It's loaded with great M & S interactions, we are introduced to the Lone Gunmen, Mulder finally speaks to Scully about Deep Throat, and it is established that DT has not only seen aliens with his own eyes, but he is one of three people on the planet who have actually exterminated them.

Plus, this is the episode where the X-files start to really fuck with their personal lives. Up to this point, TXF has just been a job to Mulder and Scully, albeit a very interesting one. But now they are being bugged, set up, misled, and their lives are starting to get a little more complicated.

It opens with this excellent exchange as M & S are investigating a UFO sighting. Mulder is gathering evidence and only half listening to Scully's ideas:
S: From the trucker’s description, the shape he fired on could conceivably have been a mountain lion.
M: Conceivably.
S: The National Weather Service last night reported atmospheric conditions in this area that were possibly conducive to lightning.
M: Possibly.
S: It is feasible that the truck was struck by lightning, creating the electrical failure.
M: It’s feasible.
S: And you know, there’s a marsh over there. The lights the driver saw may have been swamp gas.
M: Swamp gas?
I love them taking the bus after returning their rental car. I don't know why, but I think this detail is great.

The entire first part of this episode is very... playful. The intro to the Gunmen is killer:
LANGLY: Is this your skeptical partner?
FROHIKE: She’s hot.

To be fair, Frohike is right; this is easily the best Scully has looked in the whole season so far. I'm not the only one to think so!

S: Those were the most paranoid people I have ever met. I don’t know how you could think that what they say is even remotely plausible.
M: I think it’s remotely plausible that someone might think you’re hot.
...Scully has no response, just this priceless look....

Then, I don't think I have to tell you, I enjoy any time they spend at eachother's apartments. Even if they are fighting about the authenticity of UFO photos.

S:I have never met anyone so passionate and dedicated to a belief as you. It’s so intense that sometimes it’s blinding. But there are others who are watching you, who know what I know and whereas I can respect and admire your passion, they will use it against you. Mulder, the truth is out there but so are lies.
Scully is right, of course. The photos are fake, and DT is trying to throw them off track. They realize that they are totally alone one this, and they can't trust anyone else anymore. And amazingly, Scully seems to be willing to roll with the alien theories this time, she really does. It's like the ultimate trust; she doesn't really believe in this stuff, but she does believe Mulder. When Scully asks (a couple of times in this ep) if they are looking at the work of aliens, she isn't being sarcastic; she really does want to know!

Now they need to outsmart those who are playing them. They known they are being monitored, and must be evasive. Scully is shown buying a plane ticket with her credit card, then another ticket and a stopover, with cash.
An alien "rescue mission" is faked in order to throw them off. The acts of deception in this episode from both ends are complex.
They manage to find the wreckage and the EBE anyway, after stumbling upon a UFO party. It leads them to a power plant of all places, where the aliens is being held. And killed. By the time Mulder finally gets to it, it's gone. DT confesses everything- his guilt for being one of three who have killed the aliens is his motivation for helping Mulder find the truth. What DT tries so hard to hide, he also hopes one day Mulder can expose.
Oh, on an USTy note? Hotel rooms, stakeouts, both apartments. All the right ingredients. Just saying.
