1.1 Pilot: "The X-Files"
Dr. Scully is given the assignment to watch over the activities of a certain Agent Mulder and decide if his work is worthwhile to the FBI. He takes her to investigate the murder of several high school classmates in Oregon whom he believes have been experimented on by aliens.
1.2 "Deep Throat"
Mulder and Scully head out to Ellens Air Force Base in Idaho, against the wishes of some very mysterious and powerful people. The investigation begins with the disappearance of one of the test pilots and leads to the implication of possible experimentation on UFOs by the military.
A gruesome murder without motive, clear M.O., or point of entry bears resemblance to an X-File killer. However, the X-File cases took place in 1933 and 1963. Mulder and Scully attempt to track down and stop this century old killer.
A woman who claims to have seen a UFO as a child has her teenage daughter disappear while on a camping trip. The signs seem to indicate alien involvement. But the key to solving the mystery may be the woman's young son instead of the missing daughter.
1.5 "The Jersey Devil"
The discovery of a cannibalized human body in New Jersey State Park sends Mulder and Scully to Atlantic City. Despite obvious police cover-ups, Mulder continues his investigation of what may be a missing link in human evolution. Meanwhile, Scully attends her god-son's birthday party, which leads to some reflection on her future social plans.
When two very odd corpses appear in Philadelphia, Mulder and Scully are requested to take a look at them. The investigation turns up a secretary whose employer recently committed suicide and a strange force which seems to protect her.
1.7 "Ghost in the Machine"
Following the electrocution of a computer company's CEO, Mulder's old partner asks for help with the case. With the advice of Deep Throat, Mulder and Scully must stop the murderer, all the while fighting off the defense department and the building itself.
When the Arctic Ice Core project's final transmission is a crazed scientist saying "We are not who we are," Mulder and Scully become part of an investigative team sent to the Alaskan site. Upon arrival, they discover that the unearthing of an unearthly parasite could spell trouble for them as well.
After a space shuttle launch is aborted and evidence of some bizarre sabotage is found, a NASA worker asks Mulder and Scully to take a look around. Meanwhile, the former astronaut who is in charge of the mission is apparently haunted by something he encountered during a spacewalk on a previous mission.
1.10 "Fallen Angel"
Mulder is tipped off by Deep Throat about a government cover-up of a UFO crash site. He is not the only one interested, as he discovers a fellow UFO enthusiast whose appearance seems rather coincidental. So the military tries to keep Mulder away while trying to bring a certain other being in. But when he is discovered, Mulder's position in the FBI is jeopardized.
Mulder and Scully check out the curious murder of a man in Connecticut. When they discover that another man in California was killed simultaneously in the same manner, the uncanny resemblance of the two men's daughters seems more than coincidental. So, when the first child disappears, the two decide to keep an eye on the remaining child. What they find isn't alien, but rather something much more familiar.
An old flame of Mulder's tries to enlist his aid to protect a visiting Parliament member and lights a small spark of jealousy in Scully. Mulder must overcome his fear of fire to take on the hot-headed pyrokinetic serial killer.
1.13 "Beyond the Sea"
After Scully's father passes away, her skepticism is tested by a prisoner on death row who claims that by using recently gained psychic powers, he can help catch a kidnapper. Without Mulder's guidance, she must decide for herself whether or not the man's visions are truth or a by-product of her grief.
A series of sexually related killings confound the two agents who aren't certain if the murderer is male or female. The clues lead them to a small Amish-like community called the Kindred in Massachusetts who are more puzzling than the serial killer.
During a trap set for a bank robber, a fellow agent and friend of Scully's is shot by the criminal, whom Scully shoots in turn. While the agent is brought back from apparent death, he takes on the persona of the dead criminal whom he has chased for nearly a year. Scully sticks with him during his "trauma," but Mulder believes that he is not who he is.
1.16 "Young at Heart"
A criminal captured by a younger, fresh-from-the-academy Fox Mulder seems to be making good on his promise of vengeance against the agent. Now an older, wiser Mulder must attempt to find this elusive stalker who may not be wiser...or older.
After a downed UFO crashes near Iraqi airspace, an unmarked truck carrying its occupant is assailed in Tennessee, causing multiple UFO sightings. Drawn by the event, Mulder and Scully find themselves tracking the trailer, with the help and hindrance of Deep Throat.
1.18 "Miracle Man"
The inexplicable deaths of several people at the hands of a faith healer send Mulder and Scully into the Bible belt. The deaths have shaken the miracle worker's faith in his gift, but not before Mulder experiences some of the boy's power.
The shooting of a Native American draws Mulder's attention as the murderer believed he had shot an animal of some sort. But an Indian myth and some strange evidence seem to indicate the possibility of lycanthropy, the very phenomenon which opened the very first X-File.
1.20 "Darkness Falls"
Mulder pulls some strings to be assigned to a case involving the disappearance of 30 loggers in Washington state. They discover that the loggers, in illegally cutting down a tree, faced a punishment far worse than what the judicial system would have done. Now the two agents must try to avoid the same dark fate.
Eugene Tooms, a mutant killer brought in by Mulder and Scully, is released based on psychiatric re-evaluation and lack of evidence. So Mulder sets out to prevent Tooms from killing for the fifth and final liver he needs, while Scully attempts to locate more definitive evidence. Both tasks made more difficult by their superiors insistence that they work by the book.
1.22 "Born Again"
A little girl is tied to the deaths of two Buffalo policemen, but the possibility that she is the murderer is ludicrous. So Mulder and Scully begin an investigation of the eight year old, turning up evidence that may help to solve a nine year old murder case. A case Mulder believes was the death of the girl's past life.
A mentally handicapped janitor seems to be the only suspect in the murders of two members of a propulsion research team. Yet the evidence of advanced theoretical work seems to eliminate the possibility, until Mulder and Scully uncover his relationship to a scientist whose brain has been cryogenically preserved.
1.24 "The Erlenmeyer Flask"
When Deep Throat points out a news story about a fugitive who apparently drowned, Mulder and Scully cannot see what makes it special. But with his insistence, they discover evidence of secret government experimentation with extraterrestrial DNA. However, the evidence and everyone who has seen it is quickly being eliminated.