Deep Throat is the first proper episode of The X-Files, in that it features the now legendary title sequence and theme music, the catchphrase "The truth is out there" and, most importantly, the introduction of the show's famous "mythology" storyline, an arc which, unlike Twin Peaks' murder mystery, was allowed to stay partially unresolved until the definitive end of the series.
The complex ongoing plot line, which revolves around the possibility that the US government and military know about the existence of aliens and do everything in their power to hide the truth, begins when a mysterious man (Jerry Hardin), subsequently referred to as Deep Throat, approaches Mulder and advises him to suspend his most recent investigation. Mulder, being who he is, ignores the advice and follows a set of clues that lead him to an air base which supposedly contains the bodies of extraterrestrials. Once he gets there, though, he gets in more trouble than expected, and while Scully tries to save him they both realize there's a bigger secret being hidden, one that could cost them their jobs and possibly even their lives.
Unusually for a science-fiction show, The X-Files never really featured any overly heavy effects work (barring the 1998 movie), primarily because Chris Carter was more interested in the human aspect. This is especially clear in the mythology episodes, which look more like political thrillers than full-blown sci-fi blockbusters. Carter explicitly drew inspiration from the film All the President's Men, a fact that is confirmed by the informant being named Deep Throat (although the name is never actually used in this episode). The character in question is played with the right shade of mystery by Hardin, while a still-not-famous-at-the-time Seth Green provides some comic relief as a stoned teenager.
More than anything, though, this episode shows how The X-Files, like Twin Peaks before it and other serials after it, never gave any reassuring answers. Evidence of this can be found in the unsettling conversation between Mulder and Deep Throat: "They're here, aren't they?" "Mr. Mulder, they've been here for a long, long time". The rest, as they say, is television history.
