Deep Throat

"People see what they wanna see."

Written by Chris Carter
Directed by Daniel Sackheim

"When does the human cost become too high for the building of a better machine?"

— Fox Mulder

Mulder and Scully receive a request from the wife of an Air Force test pilot to investigate what has happened to her husband. Maybe the pressure of the job just got to him, but after a mysterious informant warns Mulder off the case, he decides that he has to investigate. That decision proves costly...

Tropes:

Big Damn Heroes: Scully's rescue of Mulder, achieved single-handedly against the entire Air Force Base.
Character Title: Or pseudonym in this case.
Distressed Dude: After his investigation goes sour, Mulder is captured by government forces and needs to be rescued by Scully.
Establishing Character Moment: Deep Throat's enigmatic confrontation of Mulder and cryptic manner, and for the first time, we get to see how ferociously loyal and all-around badass Scully is when she makes a split-second decision to take a government employee hostage at gunpoint and use him as a bargaining chip to rescue Mulder.

E.T. Gave Us Wi-Fi: Mulder believes that the mysterious flying objects seen in the area are airplanes built by the Air Force based on UFO technology retrieved from the Roswell Incident in 1947.
Gun Struggle: One that Scully comes out on top of.
Hero Insurance: How was Mulder not kicked out of the FBI for breaking into a top secret military base? Likely only his political connections and Deep Throat made that so.
He Was Right There All Along: Deep Throat surprising Mulder in the bathroom.
Memory-Wiping Crew: There's one in the Air Force Base, which selectively removes memories from test pilots who see more than they can handle. They also work on Mulder at the end.
Mysterious Informant: The episode introduces Deep Throat, Mulder's first government informant.

Non-Indicative Title: To the new watcher, the title makes no sense whatsoever, for it's never mentioned who or what Deep Throat exactly is.

Prisoner Exchange: Scully orchestrates one to rescue Mulder.
Shout-Out: "Deep Throat" is a well-known term for a mysterious whistleblower. Those viewers not familiar with All the President's Men may remain puzzled, however.
Stoners Are Funny: The stoner kids.
Strapped to an Operating Table: Happens to Mulder when he's captured by Air Force Base troops.
Time Skip: Although it's not obvious, this episode is time-stamped as taking place roughly 15 months after the pilot. Later episodes seemed to forget about this when mentioning how long Mulder and Scully had been partners, though.
Workout Fanservice: Mulder doing laps on the track at the end, mainly because of his bare arms.