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.