FBI Special Agent Dana Scully is assigned to work with Fox Mulder on a group of unexplained cases labeled as X-files. Mulder believes that the paranormal can explain most of the cases, whereas Scully is more interested in finding a scientific, logical explanation.
Her first case with Mulder involved a series of unexplainable deaths of young people in a small Oregon town. Mulder fears that Scully may be a spy for the higher ups at the FBI but still boldly theorizes that it is the work of extraterrestrials. Discovering a non-Human corpse in the coffin of one of the victims they exhume doesn't dissuade Scully's skepticism but as the strange occurrences such as time loss, flashes of light, and strange implants in the corpse mount up even she is willing to believe Mulder's theory a bit. When she comes to Mulder fearing she has the same marks as the victims on her own back, he tells her they are merely mosquito bites. Seeing her vulnerable and embarrassed, he asks her to stay and they get to talking. He confides about the disappearance of his sister Samantha Mulder, his FBI career and study of the supernatural & the X-Files, and of a conspiracy to suppress his work on the X-Files. Scully may not believe everything he is saying but a bond has formed between them.
They realize that one of the young people from the same graduating class, Billy Miles, has been delivering people to the woods and Mulder is present for Theresa Hoese disappearing in a bright light. While most of the evidence is stolen or burned in a fire at the motel, Scully brings back the implant made of an unidentifiable material which supports what her and Mulder experienced.
When Mulder intends to investigate pilots disappearing from Ellens Air Base in Idaho, an enigmatic man warns him not to look into because the military won't tolerate an FBI investigation. Mulder ignores him so he and Scully go to Idaho and learn that the Air Force may be using planes with alien technology in them. Vehicles so advanced that the Human body can't take it and the missing pilots were wash-outs who had to have their memories altered. Mulder gets too close to all of this and his memory is altered.
Back in DC, the mystery man again meets Mulder and explains his purpose is provide information in service of the truth. He tells Mulder that the aliens have been here for a long time. Mulder refers to him as Deep Throat and it starts a useful partnership where Deep Throat gives whatever information he chooses to give despite clearly knowing far more than he ever tells Mulder and Scully. While he sometimes tips Mulder off during an investigation, he would lie on other occasions. Such as his deliberate misleading of Mulder during their hunt for a UFO downed by an Iraqi fighter jet.
While Mulder and Scully's pursuit of information on aliens often is prevented by government or military intervention, their other investigations usually prove more fruitful. Such as their apprehension of Eugene Victor Tooms, a strange mutant and serial killer who would be killed by Mulder after his later release.
Their alien investigations had a sudden break due to the fugitive Dr. William Secare. Secare leads a police chase to the waterfront and his shot before jumping into the water. But his body is not recovered. Deep Throat insists that Mulder investigate despite Mulder not knowing what it is he should be looking for. After Dr. Terrance Allen Berube is questioned by Scully and Mulder about why his car was being used by Secare, Berube is murdered. Though staged to look like a suicide, looking around at his trashed laboratory, Mulder knows it must have been murder given the man's obsession with his work and maintaining an immaculate lab. Mulder finds an erlenmeyer flask with the label "Purity Control" and gives it to Scully to check out, while he searches Berube's house.
Mulder pretends to be Berube when Secare calls Berube's home but fails to get Secare's location before he collapses at a pay phone. He follows another lead taking him to a storage facility where he finds five tanks with men suspended in liquid. And sixth empty tank. Elsewhere, Scully is being told by Dr. Anne Carpenter that the contents of the flask are extraterrestrial due to extra base pairs. When Mulder leaves the storage facility, he is chased by men in black but he evades them.
Mulder and Scully visit the storage facility the next day and it is just an empty room. Deep Throat shows up and reveals that Berube was performing gene therapy on terminally ill patients using alien viruses, transforming them into alien human hybrids. This was going too far with the work and they ordered the hybrids destroyed, but Berube had included his dying friend Dr. Secare as one of patients and helped him escape. Deep Throat hadn't told them this earlier because he didn't realize the clean-up team would be this quick. He urges them to get whatever evidence they can to expose the truth of what he revealed to them. Otherwise it is just a story.
Mulder finds Dr. Secare but the man is shot to death by one of the clean-up team. The toxic fumes from Secare's now alien body chemistry blinds Mulder. Scully learns that Carpenter and her whole family were killed in a car crash and the flask is surely missing. Deep Throat helps Scully obtain an alien embryo to trade for Mulder. Deep Throat makes the exchange but is shot and left for dead. His last words to Scully are, "Trust no one." Weeks after this the X-Files are shut down.
Episodes marked with a double dagger (‡) are episodes in the series' alien mythology arc.
|1.01||1||"Pilot"‡||Chris Carter||Robert Mandel||September 10, 1993|
|Dana Scully is assigned to work with Fox Mulder, an FBI agent with an interest in the paranormal. Together, they travel to Oregon where Mulder believes several teenagers have been abducted by aliens.||U.S. viewers (millions): 12.0 million / Rating/Share: 7.9|
|1.02||2||"Deep Throat"‡||Chris Carter||Daniel Sackheim||September 17, 1993|
|When Mulder and Scully investigate a possible conspiracy in the U.S. Air Force, a mysterious character helps Mulder to differentiate between fact and fiction.||U.S. viewers (millions): 11.1 million / Rating/Share: 7.3|
|1.03||3||"Squeeze"||Glen Morgan & James Wong||Harry Longstreet||September 24, 1993|
|Mulder and Scully investigate a serial killer who has been active since at least 1903 and is capable of squeezing his body through narrow gaps.||U.S. viewers (millions): 11.1 million / Rating/Share: N/A|
|1.04||4||"Conduit"||Alex Gansa & Howard Gordon||Daniel Sackheim||October 1, 1994|
|Mulder becomes personally connected when he and Scully encounter a young boy who is deeply affected by the disappearance, or abduction, of his teenage sister.||U.S. viewers (millions): 9.2 million / Rating/Share: N/A|
|1.05||5||"The Jersey Devil"||Chris Carter||Joe Napolitano||October 9, 1993|
|While investigating a seemingly cannabilistic murderer, Mulder and Scully encounter a beast woman.||U.S. viewers (millions): 10.4 million / Rating/Share: N/A|
|1.06||6||"Shadows"||Glen Morgan & James Wong||Michael Katleman||October 22, 1993|
|When two extremely odd corpses appear in Philadelphia, Mulder and Scully investigate the deaths and meet a female secretary who seems to be protected by a strange invisible force.||U.S. viewers (millions): 8.8 million / Rating/Share: N/A|
|1.07||7||"Ghost in the Machine"||Alex Gansa & Howard Gordon||Jerrold Freedman||October 29, 1993|
|The agents must survive in a building that is controlled by a murderous computer.||U.S. viewers (millions): 9.5 million / Rating/Share: N/A|
|1.08||8||"Ice"||Glen Morgan & James Wong||David Nutter||November 5, 1993|
|In an Arctic research station, Mulder and Scully are threatened by primordial ice worms that cause their hosts to become dangerously paranoid.||U.S. viewers (millions): 10.0 million / Rating/Share: N/A|
|1.09||9||"Space"||Chris Carter||William Graham||November 12, 1993|
|When Mulder and Scully are told of sabotage attempts to NASA Space Shuttles, the agents investigate the reports and find that the space agency may be under alien control.||U.S. viewers (millions): 10.7 million / Rating/Share: N/A|
|1.10||10||"Fallen Angel"‡||Howard Gordon & Alex Gansa||Larry Shaw||November 19, 1993|
|Mulder is informed about a government cover-up of a UFO crash site, but finds that a fellow UFO enthusiast is also interested in the find.||U.S. viewers (millions): 8.8 million / Rating/Share: N/A|
|1.11||11||"Eve"||Kenneth Biller & Chris Brancato||Fred Gerber||December 10, 1993|
|The agents encounter two girls who look identical and whose individual fathers were murdered in similar, odd circumstances at the same moment over 3000 miles apart.||U.S. viewers (millions): 10.4 million / Rating/Share: 6.8|
|1.12||12||"Fire"||Chris Carter||Larry Shaw||December 17, 1993|
|Mulder must overcome his phobia of fire to catch a mutant killer with fire-controlling capabilities.||U.S. viewers (millions): 11.1 million / Rating/Share: 6.8|
|1.13||13||"Beyond the Sea"||Glen Morgan & James Wong||David Nutter||January 7, 1994|
|After Scully's father dies, her skepticism is put to the test by a prisoner on death row who claims that by using recently gained psychic powers, he can help catch a kidnapper.||U.S. viewers (millions): 10.8 million / Rating/Share: 6.8|
|1.14||14||"Gender Bender"||Larry Barber & Paul Barber||Rob Bowman||January 21, 1994|
|Mulder and Scully investigate an enclosed community called the Kindred who appear to have the ability to switch gender.||U.S. viewers (millions): 11.1 million / Rating/Share: N/A|
|1.15||15||"Lazarus"||Alex Gansa & Howard Gordon||David Nutter||February 4, 1994|
|After a fellow agent and friend of Scully's is shot by a criminal who Scully shoots in turn, the agent is revived but Mulder suspects that he is not who he appears to be.||U.S. viewers (millions): 12.1 million / Rating/Share: N/A|
|1.16||16||"Young at Heart"||Scott Kaufer and Chris Carter||Michael Lange||February 11, 1994|
|Mulder must stop an elusive stalker who he captured in his youth, but who seems to have remained the same age.||U.S. viewers (millions): 11.5 million / Rating/Share: N/A|
|1.17||17||"E.B.E."‡||Glen Morgan & James Wong||William Graham||February 18, 1994|
|After a downed UFO crashes near Iraqi airspace, Mulder and Scully follow an unmarked truck carrying the UFO's occupant.||U.S. viewers (millions): 11.7 million / Rating/Share: N/A|
|1.18||18||"Miracle Man"||Chris Carter & Howard Gordon||Michael Lange||March 18, 1994|
|Mulder and Scully encounter a religious healer who seems to have the power to perform miracles.||U.S. viewers (millions): 11.6 million / Rating/Share: N/A|
|1.19||19||"Shapes"||Marilyn Osborn||David Nutter||April 1, 1994|
|The shooting of a Native American draws Mulder and Scully into mystery involving lycanthropy, the phenomenon that opened the X-files.||U.S. viewers (millions): 11.5 million / Rating/Share: N/A|
|1.20||20||"Darkness Falls"||Chris Carter||Joe Napolitano||April 15, 1994|
|The agents become trapped in a forest where thirty loggers strangely disappeared, with the same fate eerily approaching them.||U.S. viewers (millions): 12.5 million / Rating/Share: N/A|
|1.21||21||"Tooms"||Glen Morgan & James Wong||David Nutter||April 22, 1994|
|Eugene Victor Tooms - a limb-stretching serial killer who Mulder previously captured - is released from prison and set free against Mulder's advice.||U.S. viewers (millions): 13.4 million / Rating/Share: N/A|
|1.22||22||"Born Again"||Howard Gordon & Alex Gansa||Jerrold Freedman||April 29, 1994|
|The agents investigate an eight year old girl who is associated with the killings of two policemen that Mulder suspects murdered her past reincarnation, police officer Charlie Morris.||U.S. viewers (millions): 13.7 million / Rating/Share: N/A|
|1.22||23||"Roland"||Chris Ruppenthal||David Nutter||May 1, 1994|
|The agents encounter a mentally handicapped janitor who is the only suspect in the murders of two propulsion research scientists, but the evidence of advanced theoretical work astounds Mulder and Scully as to the killer's real identity.||U.S. viewers (millions): 12.5 million / Rating/Share: 7.9|
|1.24||24||"The Erlenmeyer Flask"‡||Chris Carter||R.W. Goodwin||May 8, 1994|
|The agents discover evidence of secret government experimentation with alien DNA, but the evidence and everyone who has seen it are quickly being eliminated.||U.S. viewers (millions): 14.0 million / Rating/Share: 8.8|
- David Duchovny as Special Agent Fox Mulder (24/24 episodes)
- Gillian Anderson as Special Agent Dana Scully (24/24 episodes)
- Jerry Hardin as Deep Throat (7/24 episodes)
- William B. Davis as Cigarette Smoking Man (4/24 episodes)
- Charles Cioffi as Division Chief Scott Blevins (2/24 episodes)
- Doug Hutchison as Eugene Victor Tooms (2/24 episodes)
- Henry Beckman as Detective Frank Briggs (2/24 episodes)
- Mitch Pileggi as Assistant Director Walter Skinner (1/24 episodes)
- Dean Haglund as Richard Langly (1/24 episodes)
- Tom Braidwood as Melvin Frohike (1/24 episodes)
- Bruce Harwood as John Fitzgerald Byers (1/24 episodes)
- With the exception of "Ice", all episodes were initially broadcast on a Friday.