In this television series, FBI agents Fox Mulder (David Duchovny) and Dana Scully (Gillian Anderson) investigate cases linked to the paranormal, called X-Files.

In this episode, the pair investigate a possible conspiracy in the United States Air Force, and Mulder meets a mysterious informant who warns him to stay away from the case.

It contains several special effects that Chris Carter later described as "good, given the [series'] restrictions";[1] although he singled out the scenes featuring blinking lights as being poorly executed.

Four months later, FBI agents Fox Mulder (David Duchovny) and Dana Scully (Gillian Anderson) meet at a Washington bar to discuss the case.

While using the bar's restroom, Mulder is approached by a mysterious informant named "Deep Throat" (Jerry Hardin), who cautions him to avoid the case.

Mulder and Scully travel to Idaho and meet with Budahas' wife, Anita, who claims her husband exhibited erratic behavior before his disappearance.

As Mulder treats Emil and Zoe to a meal at the diner, they tell the agents about the lights and how they believe the UFOs are launched from another nearby base.

[1] The UFO was digitally constructed, based around what visual effects supervisor Mat Beck described as a "sort of disco light rig" that was rented from a "party supplier".

[5] The house used for the exterior shots of the Budahas residence was reused in Carter's next series, Millennium, as the home of protagonist Frank Black.

[8] The initial scene with Duchovny and Anderson in the bar was shot at a Vancouver restaurant called The Meat Market, which according to Carter was a much "divier location than the production designers would have you believe".

Only key grip Al Campbell made use of this bus service, causing producers to abandon the idea until the fourth season episode "Herrenvolk".

[2] Mossinger's warning to Mulder that some truths should be kept hidden from the public has been cited by scholars as representing the difficulty of forcing large organizations to take responsibility for wrongdoing.

This trend has replaced traditional science fiction topics such as space exploration with themes inspired by the Watergate scandal and the spread of conspiracy theories.

[23] The Toronto Star's Mike Antonucci wrote that the episode demonstrates that Carter "can blend subtle, complicated elements with heart-pounding action", adding that "Nothing is obvious about The X-Files, in fact, except its quality".

[24] Michael Janusonis of The Beaver County Times was more critical, calling it "an acquired taste" and noting that it "sort of diddled out in the end", lacking "a completely satisfactory resolution".

[26] Writing for website Den of Geek, Matt Haigh reviewed the episode positively, praising its decision not to answer all the questions it asks.

Haigh noted that "the fact that we are left as clueless about what really happened as Mulder and Scully only enhances the viewing experience", finding such mystery to be "a rare thing indeed" on network television.

[28] Shearman felt that the episode was "a skillfully scripted story of cover-up and paranoia", and noted that "it sets up the overall themes of the show so well, it almost seems like a primer".

[29] IGN's Dan Iverson felt that the episode served to "open the door to the possibilities of this series";[20] while Tor.com's Meghan Deans noted that "although the pilot introduced the idea of government conspiracy, it's 'Deep Throat' that kicks out the edges of the canvas".