The X-Files, S1E2 - "Deep Throat"

The first post-pilot episode of The X-Files covers similar territory to the pilot, chiefly because the series is still going through some necessary world-building to lay the groundwork for the overall arc about aliens and government conspiracy. Mulder's attention has been drawn to the case of Colonel Budahas, a pilot at Ellens Air Base in Idaho, who vanished into government custody four months ago after a psychotic episode. He convinces Scully to investigate with him, but before they depart, an unknown man (identified by the series only as "Deep Throat") warns Mulder that getting involved in the case could be dangerous to him and Scully, and suggests that he could be of help to Mulder in the future. The introduction of Deep Throat, as well as the suggestions that Mulder's phone might be monitored, increase the show's sense of paranoia and add a level of depth to the conspiracy.

Arriving at Ellens Air Base, Mulder and Scully interview Colonel Budahas' wife, who recounts to them how her husband was involved in secret military work, and how he began to appear mentally unwell prior to his disappearance. The agents attempt to interview a Colonel Kissell about the disappearance, only to be rebuffed, and encounter a local reporter named Paul Mossinger. At a local dive bar, Mulder purchases a photograph, purportedly of a UFO, and receives directions to a spot overlooking the base where, at night, Mulder and Scully see some lights in the sky moving in ways impossible for normal aircraft. The agents are chased away from the base by a helicopter, in the process meeting two stoner kids named Zoe and Emil (played by Seth Green in typical but amusing form). They inform the agents that the lights are a frequent occurrence over the base, suggesting that they could be experimental technology developed at a secret location they dub "Yellow Base." Mulder makes a connection to the Roswell incident of 1947, comparing a UFO sighted over Roswell to the one in the photo he purchased, and theorizing that Ellens Air Base are developing experimental craft from alien technology taken from Roswell, and that Colonel Budahas and pilots like him experienced averse physical reactions to flying these aircraft.

The agents then receive word that Colonel Budahas has returned home. The Colonel's wife is adamant that the man before them is not her husband, and that something has been done to him by the government. The Colonel is unable to answer questions or remember information about piloting aircraft, leading Mulder to speculate that the government removed sensitive information from his memory. The agents are accosted by a group of men (suggested to be the Men in Black, or an equivalent), who take evidence from them and instruct them to return to Washington immediately or face consequences. Mulder discloses his visit from Deep Throat to Scully and speculates that Colonel Budahas was returned to his wife to get them off the case and keep them from investigating the experimental aircraft further. Mulder then runs off to investigate on his own, arriving at Yellow Base and witnessing firsthand one of the mystery aircraft (the result of some early-nineties CGI that has aged far less well than the rest of the episode). Mulder is discovered by the military stationed at the base, and is taken into custody and drugged. Scully attempts to find Mulder's whereabouts and has another encounter with Paul Mossinger, who is revealed to be working for the base security. Scully holds him at gunpoint and demands that he take her to Mulder. Mulder is released to Scully, but is unable to remember what happened inside the base, having had his memory of it removed.

Returning to Washington, Scully submits her report to the Bureau, while Mulder has another encounter with Deep Throat. The enigmatic gentleman warns Mulder that caution will be required now that he has witnessed things he was not meant to, but offers him information that can help in his quest for the Truth. Finally, he confirms Mulder's belief in aliens, stating that "they've been here a long, long time."

As a whole, "Deep Throat" builds upon the themes and elements introduced in the pilot. It integrates various elements of ufology into the series' mythos, including Roswell, the development of experimental aircraft derived from alien technology, and shadowy government and military forces willing to do anything to protect their secrets. It also introduces us to Deep Throat, a character every bit as enigmatic and connected to conspiracy as the Smoking Man, but who proves a valuable ally to Mulder and Scully. Finally, the temporary abduction of Mulder allows the audience to see some of the lengths Scully will go to to protect him, helping to solidify the relationship between the two.