The X-Files, S1E4 - "Conduit"

"Conduit" opens with Division Chief Blevins informing Scully of Mulder's request for funds to investigate the disappearance of a teenage girl named Ruby Morris in Sioux City, Iowa. Blevins suggests that Mulder is drawing a parallel to the disappearance of his own sister and seeks to deny the request; Scully convinces him to let her speak to Mulder first. Mulder reveals that the location of the disappearance, Lake Okobogee, was the site of multiple UFO sightings in 1967, including by Ruby Morris's mother, Darlene. The agents travel to Sioux City and meet with Darlene Morris, who believes that her daughter was taken by aliens. Mulder discovers that Darlene's son, Kevin, has begun writing out sequences of binary code; he claims that they are messages he is receiving from the television. Mulder sends a copy of the binary code back to Washington for analysis.

Local law enforcement prove not to be overly concerned with the disappearance of Ruby Morris, believing that she ran away due to her history of delinquency. The agents then encounter a young woman named Tessa, who tells them that Ruby was pregnant by a boyfriend named Greg Randall, a local bartender. The agents look for Randall at his workplace, only to be informed that he has been missing. That night, Mulder and Scully are confronted at their hotel by NSA agents, who inform them that the binary sequence Kevin wrote was a transmission from a defense satellite, and that Kevin is now considered a potential national security risk. The NSA raid the Morris home and take Darlene and Kevin into custody; before leaving the house, Mulder notices that the roof of Darlene's camper, where she was sleeping the night of the abduction, is burned. Upon analysis, Kevin's binary writings prove to translate into a variety of data fragments, including images, text, and audio samples. Darlene and Kevin are released, but Darlene is no longer trusting of Mulder and Scully. Mulder posits that Kevin's proximity to Ruby when she was abducted turned him into a conduit for data, causing him to receive information from the television. Mulder and Scully travel to Lake Okobogee to investigate, noticing burned trees and traces of sand fused into glass, evidence of extreme heat. In the nearby woods, the agents also discover a grave, which proves to contain the body of Greg Randall. Randall's wallet contains a note which the agents establish was written by Tessa.

Tessa is brought in for questioning. The agents determine that she, not Ruby, was pregnant by Greg, and Mulder accuses her of killing Greg because he was cheating on her with Ruby. Tessa confesses to killing Greg, but not Ruby. Scully remains convinced that Ruby is dead, but Mulder believes that she is alive but abducted. The agents return to the Morris house, only the find Darlene and Kevin gone, with Kevin leaving behind a giant picture of Ruby formed by binary code. The agents return to Lake Okobogee and find Darlene in the woods. Mulder narrowly rescues Kevin from being run over by a rally of bikers, and Scully and Darlene discover Ruby nearby, alive but in a coma.

Ruby awakens at the hospital, and is discovered to possess signs of prolonged weightlessness. Mulder and Scully attempt to talk to her about her experience, but they are turned away by Darlene. Mulder argues that Ruby needs to be allowed to reveal the truth; Darlene counters that telling the truth about her own UFO experience has only ever brought her ridicule. The agents return to Washington, and the episode ends with Scully listening to the tapes of Mulder's hypnotherapy regarding his sister's disappearance while Mulder breaks down in a church. The tape concludes with Mulder remembering a voice telling him that his sister will come to no harm; the therapist asks if he believes the voice, to which he simply replies, "I want to believe."

In terms of its plot, "Conduit" is heavy on red herrings: Tessa and Greg prove to have no connection to Ruby's disappearance, and even Kevin's newfound ability to receive data fragments from the television has no real impact on the ultimate resolution of the story, apart from giving Mulder and Scully the clue to go to Lake Okobogee at the climax. The real purpose of the episode is to explore Mulder's character, delving into the abduction of his sister and showing how it causes him to sympathize with Darlene over her daughter's disappearance. The ending also addresses the potential consequences of "the Truth," and how Darlene's desire to protect her daughter contrasts and conflicts with the way Mulder has sought the truth without regard for his own reputation. Finally, we are given Mulder's firsthand account of his sister's abduction, the event that has shaped his entire background as a character, as well as some context for those iconic words, "I want to believe." Mulder does not just desire for aliens to be real; he believes out of hope for his sister, and that his entire life's work might someday have real consequence.

The X-Files, S1E3 - "Squeeze"

We begin with Scully having lunch with an old colleague from the FBI Academy, Agent Tom Colton, who asks for her help in solving a series of murders in the Baltimore area. In all cases, the victims were found dead in a completely locked room with their liver removed. Colton is immediately established as a self-promoter, dedicated to raising himself through the ranks of the FBI, suggesting his ultimate role in the episode, as an obstacle to Scully and especially Mulder. While investigating the scene of the latest murder, Mulder discovers an elongated fingerprint, which he matches to ones discovered at murder scenes in 1963 and 1933. Mulder establishes that every 30 years, beginning in 1903, five murders are performed, always with the liver taken from the victims. Based on the fingerprints, he believes that the same person is responsible for all of the killings.

Scully suggests to the agents in charge of the investigation that the killer may return to the scenes of previous murders, so a stakeout is called. Mulder arrives and discovers a man crawling out of an air duct, who is arrested and identified as Eugene Victor Tooms. Tooms passes a polygraph test and is released, with Colton and the other agents dismissive of Mulder's insistence that Tooms is responsible for both the current and past murders. The continued attitude of disrespect toward Mulder by other agents is clearly intended to show the audience firsthand what had previously only been alluded to - the degree to which Mulder is looked down upon by the rest of the FBI - but it grows tiresome quickly. Continuing to investigate, Mulder discovers that Tooms' fingerprint is a match for the elongated one found at the scene of the murder. That night, Tooms strikes again, revealing his ability to contort his body into impossibly small spaces.

Seeking further evidence, Mulder discovers Tooms' name on a census record from 1903, listed as living in the same apartment building as the first victim. Scully theorizes that the 1903 Tooms is the present-day Tooms' ancestor; Mulder remains convinced the murders were all carried out by the same person. The agents then seek out an interview with Frank Briggs, a detective who investigated the murders in 1933. Briggs, played by Henry Beckman, is a highlight of the episode, telling a chilling story of his investigation into the murders. He gives Mulder and Scully evidence he collected regarding the 1963 murders, including photographs of Tooms, who has not aged in 30 years. The agents investigate Tooms' old apartment building, where they find a nest constructed of rags and newspaper held together with human bile. Mulder speculates that Tooms is a genetic mutant who hibernates in the nest, awakening every thirty years to consume five livers for survival. Mulder and Scully leave, unaware that Tooms has marked Scully for his next victim.

Mulder and Scully order a stakeout on Tooms' residence, but Colton calls it off without telling them. Scully returns home and attempts to contact Mulder, while Tooms enter her apartment. Mulder arrives for the stakeout and discovers Scully's pendant in Tooms' nest, at the same time as Tooms attacks Scully (the image of the crazed Tooms diving out of a heating vent is nothing if not memorable). Mulder arrives at Scully's apartment in time to fight off and apprehend Tooms. Mulder and Scully later consult outside of Tooms' jail cell, where he has already begun building a new nest. Scully reveals that Tooms' possesses skeletal and muscular abnormalities, as well as a declining metabolism, while Mulder philosophizes about how peoples' best efforts to keep themselves safe in their homes are useless against a creature like Tooms. The agents depart, and Tooms is left to contemplate escape.

"Squeeze" is the first episode of The X-Files to divert from the overarching alien conspiracy plotline, establishing that there are many more strange and paranormal elements at work in the X-Files universe. Tooms himself remains a memorable monster, thanks in large part to Doug Hutchison's quietly sinister performance. Finally, the episode allows Scully to show her loyalty to Mulder, defending him against the ruthless career advancer Colton.

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.

The X-Files, S1E1 - "Pilot"

The X-Files opens with medical wunderkind Dana Scully assigned to work with Fox Mulder, a talented psychological profiler with an abiding obsession with the X-Files, the FBI's collection of cases dealing with the unexplained and paranormal. From their first scene together, Mulder and Scully's identities are firmly established: Mulder is the believer in the unexplained and paranormal, determined to find the truth, while Scully is the skeptic, always seeking answers in the realm of the rational. The two are clearly indicated to be equal opposites (or perhaps complements), not opponents, always a key part of their dynamic. This first interaction also introduces two other key elements: the oft-repeated words "I Want To Believe," written on Mulder's UFO poster, whose deeper meaning would not be explored just yet, and Mulder's concept of "The Truth," one of the overarching themes of the series.

On their first venture together, Mulder and Scully travel to a small town in Oregon, where several members of the Class of 1989 have turned up dead in mysterious circumstances. Mulder finds his attention drawn to the latest victim, who had strange markings on her body containing an unidentifiable chemical compound. Noting that the previous three victims were autopsied by a different medical examiner than the last, a Dr. Nemman, Mulder suspects the doctor of concealing evidence and orders one of the bodies exhumed. Despite resistance from Nemman, the agents unearth the coffin of victim Ray Soames, discovering a clearly inhuman corpse with a metal object implanted in its skull. Continuing their investigations, the agents discover two more members of the Class of 1989 in a mental institution: the comatose Billy Miles and Peggy O'Dell, who also bears the same markings on her body, matching a prediction by Mulder. It is here that Mulder first voices his opinion to Scully that the victims are being abducted by aliens, who are responsible for the markings. Scully decides that they should investigate the forest where the victims were found, where the agents discover an unknown substance on the ground and encounter a hostile local detective.

Later that night, Mulder discloses to Scully the motivation for his obsession with the X-Files: his sister vanished as a child, and he believes she was abducted by aliens. He also reveals that an unknown party within the government is attempting to thwart his investigations, and that the current case is the closest he has ever come to finding true evidence of extraterrestrials. This scene is an important one, not only because it establishes the abduction of Mulder's sister as the key formative event for his character, but because it lays down the two key elements of the X-Files universe: the possible existence of aliens, and the conspiracy by the government to conceal this knowledge. The agents are interrupted by an anonymous call that Peggy O'Dell has been killed; the agents discover that the previously wheelchair-bound girl ran in front of a truck not far from the forest where the other victims were killed. Mulder gets a call that the inhuman corpse has been stolen, and the agents return to their motel to find it engulfed in flames and their findings destroyed. Dr. Nemman's daughter, Theresa, approaches them and asks for help, revealing that she bears the markings and fears that she will be killed next. Dr. Nemman arrives to take her home, along with the hostile detective, who is revealed to be Billy Miles' father. Mulder and Scully attempt to investigate the graves of the other victims, only to discover that they have been dug up and the bodies stolen. Mulder begins to suspect Billy Miles of taking the victims into the forest, where he believes they are subjected to tests by an unknown force, causing the mutations they observed in the corpse.

The agents check in on Billy Miles, discovering the substance from the forest on his body, proving that he was there the previous night. The agents return to the forest to collect further samples, but are threatened by Billy's father. Hearing screams, the agents discover Billy Miles with Theresa Nemman. A blinding light appears, then vanishes, leaving Billy healed from his coma with the markings gone from his body. Under hypnosis, Billy reveals that he and the other victims had all experience "the light" at a party, and that it had compelled him to bring the others to the forest through an implant in his head. Returning to Washington, Scully presents her Division Chief with the implant from the corpse, the only piece of evidence she was able to save. Mulder calls Scully to tell her that their casefile on Billy Miles has vanished, evidence that someone is working against them, and the implant is filed away in the bowels of the Pentagon by a sinister figure: the individual who would go on to be named as the Smoking Man. The Smoking Man's role in this episode is effective: he has no dialogue and is not named, but simply stands present at key moments, whispering words of instruction to members of the Bureau. This establishes him right from the beginning as an elusive figure with powerful connections, a role that would be greatly expanded on in the future.