• Episode Number: 1
• Original Air Date: September 10, 1993
• Written by: Chris Carter
• Directed by: Robert Mandel
• Guest Cast:
  • Zachary Ansley (Billy Miles)
  • Charles Cioffi (Section Chief Scott Blevins)
  • William B. Davis (Smoking Man)
  • Cliff DeYoung (Dr. Jay Nemman)
  • Sarah Koskoff (Theresa Nemman)

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.

    1.02 "Deep Throat"

• Episode Number: 2
• Original Air Date: September 17, 1993
• Written by: Chris Carter
• Directed by: Daniel Sackheim
• Guest Cast:
  • Charles Cioffi (Section Chief Scott Blevins)
  • Michael Bryan French (Paul Mossinger)
  • Seth Green (Emil)
  • Jerry Hardin (Deep Throat)
  • Andrew Johnston (Col. Robert Budahas)
  • Lalainia Lindejerg (Zoe)
  • Vince Metcalfe (Kissell)
  • Monica Parker (Ladonna)

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.

    1.03 "Squeeze"

• Episode Number: 3
• Original Air Date: September 24, 1993
• Written by: Glen Morgan & James Wong
• Directed by: Harry Longstreet
• Guest Cast:
  • Henry Beckman (Detective Frank Briggs)
  • Donal Logue (Agent Tom Colton)

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.

    1.04 "Conduit"

• Episode Number: 4
• Original Air Date: October 01, 1993
• Written by: Alex Gansa & Howard Gordon
• Directed by: Daniel Sackheim
• Guest Cast:
  • Michael Cavanaugh (Sioux City Sheriff)
  • Charles Cioffi (Section Chief Scott Blevins)
  • Taunya Dee (Ruby)
  • Don Gibb (Pennsylvania Pub Bartender)
  • Shelley Owens (Tessa)
  • Joel Palmer (Kevin Morris)
  • Carrie Snodgress (Darlene Morris)

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.

    1.05 "The Jersey Devil"

• Episode Number: 5
• Original Air Date: October 08, 1993
• Written by: Chris Carter
• Directed by: Joe Napolitano
• Guest Cast:
  • Michael MacRae (Ranger Peter Brullet)
  • Gregory Sierra (Dr. Diamond)
  • Claire Stansfield (Creature)

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.

    1.06 "Shadows"

• Episode Number: 6
• Original Air Date: October 22, 1993
• Written by: Glen Morgan & James Wong
• Directed by: Michael Katleman
• Guest Cast:
  • Barry Primus (Robert Dorlund)

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.

    1.07 "Ghost in the Machine"

• Episode Number: 7
• Original Air Date: October 29, 1993
• Written by: Alex Gansa & Howard Gordon
• Directed by: Jerrold Freedman
• Guest Cast:
  • Gillian Barber (Agent Nancy Spiller)
  • Wayne Duvall (Agent Jerry Lamana)
  • Jerry Hardin (Deep Throat)
  • Rob LaBelle (Brad Wilczek)

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.

    1.08 "Ice"

• Episode Number: 8
• Original Air Date: November 05, 1993
• Written by: Glen Morgan & James Wong
• Directed by: David Nutter
• Guest Cast:
  • Xander Berkeley (Dr. Hodge)
  • Felicity Huffman (Dr. Nancy DaSilva)
  • Steve Hytner (Dr. Denny Murphy)

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.

    1.09 "Space"

• Episode Number: 9
• Original Air Date: November 12, 1993
• Written by: Chris Carter
• Directed by: William Graham
• Guest Cast:
  • Ed Lauter (Lt. Col. Marcus Aurelius Belt)

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"

• Episode Number: 10
• Original Air Date: November 19, 1993
• Written by: Howard Gordon & Alex Gansa
• Directed by: Larry Shaw
• Guest Cast:
  • Marshall Bell (Col. Calvin Henderson)
  • Scott Bellis (Max Fenig)
  • Frederick Coffin (Section Chief Joseph McGrath)

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.

    1.11 "Eve"

• Episode Number: 11
• Original Air Date: December 10, 1993
• Written by: Kenneth Biller & Chris Brancato
• Directed by: Fred Gerber
• Guest Cast:
  • Jerry Hardin (Deep Throat)
  • Harriet Harris (Dr. Sally Kendrick/Eve 6,7,8)
  • Erika Krievens (Cindy Reardon)

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.

    1.12 "Fire"

• Episode Number: 12
• Original Air Date: December 17, 1993
• Written by: Chris Carter
• Directed by: Larry Shaw
• Guest Cast:
  • Dan Lett (Sir Malcolm Marsden)
  • Laurie Paton (Lady Marsden)
  • Amanda Pays (Inspector Phoebe Green)

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"

• Episode Number: 13
• Original Air Date: January 07, 1994
• Written by: Glen Morgan & James Wong
• Directed by: David Nutter
• Guest Cast:
  • Don S Davis (Captain William Scully)
  • Brad Dourif (Luther Lee Boggs)
  • Lawrence King (Lucas Jackson Henry)

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.

    1.14 "GenderBender"

• Episode Number: 14
• Original Air Date: January 21, 1994
• Written by: Larry Barber & Paul Barber
• Directed by: Rob Bowman
• Guest Cast:
  • Michele Goodger (Sister Abigail)
  • Brent Hinkley (Brother Andrew)
  • Peter Stebbings (Marty [Male])

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.

    1.15 "Lazarus"

• Episode Number: 15
• Original Air Date: February 04, 1994
• Written by: Alex Gansa & Howard Gordon
• Directed by: David Nutter
• Guest Cast:
  • Christopher Allport (Agent Jack Willis)
  • Jackson Davies (Agent Ruskin)
  • Jason Schombing (Warren James Dupre)

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"

• Episode Number: 16
• Original Air Date: February 11, 1994
• Written by: Scott Kaufer & Chris Carter
• Directed by: Michael Lange
• Guest Cast:
  • Alan Boyce (Young John Barnett)
  • Christine Estabrook (Agent Henderson)
  • Jerry Hardin (Deep Throat)
  • Graham Jarvis (Doctor at N.I.H.)
  • Robin Mossley (Dr. Joe Ridley)
  • David Petersen (Older John Barnett)
  • Gordon Tipple (Joe Crandall)

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.

    1.17 "E.B.E."

• Episode Number: 17
• Original Air Date: February 18, 1994
• Written by: Glen Morgan & James Wong
• Directed by: William Graham
• Guest Cast:
  • Tom Braidwood (Frohike)
  • Dean Haglund (Langly)
  • Jerry Hardin (Deep Throat)
  • Bruce Harwood (Byers)

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"

• Episode Number: 18
• Written by: Howard Gordon & Chris Carter
• Directed by: Michael Lange
• Guest Cast:
  • Scott Bairstow (Samuel Hartley)
  • R.D. Call (Sheriff Maurice Daniels)
  • George Gerdes (Reverend Calvin Hartley)

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.

    1.19 "Shapes"

• Episode Number: 19
• Original Air Date: April 01, 1994
• Written by: Marilyn Osborn
• Directed by: David Nutter
• Guest Cast:
  • Jimmy Herman (Ish)
  • Michael Horse (Sheriff Charles Tskany)
  • Ty Miller (Lyle Parker)
  • Renae Morriseau (Gwen Goodensnake)

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"

• Episode Number: 20
• Original Air Date: April 15, 1994
• Written by: Chris Carter
• Directed by: Joe Napolitano
• Guest Cast:
  • Jason Begh (Larry Moore)
  • Barry Greene (Perkins)
  • Tom O'Rourke (Steve Humphreys)
  • Ken Tremblett (Dyer)

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.

    1.21 "Tooms"

• Episode Number: 21
• Original Air Date: April 22, 1994
• Written by: Glen Morgan & James Wong
• Directed by: David Nutter
• Guest Cast:
  • Henry Beckman (Detective Frank Briggs)
  • William B. Davis (Smoking Man)
  • Doug Hutchison (Eugene Victor Tooms)

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"

• Episode Number: 22
• Original Air Date: April 29, 1994
• Written by: Howard Gordon & Alex Gansa
• Directed by: Jerrold Freedman
• Guest Cast:
  • P. Lynn Johnson (Dr. Sheila Braun)
  • Mimi Lieber (Anita Fiore)
  • Andrea Libman (Michelle Bishop)
  • Brian Markinson (Tony Fiore)
  • Maggie Wheeler (Detective Sharon Lazard)

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.

    1.23 "Roland"

• Episode Number: 23
• Original Air Date: May 06, 1994
• Written by: Chris Ruppenthal
• Directed by: David Nutter
• Guest Cast:
  • Garry Davey (Dr. Keats)
  • Zeljko Ivanek (Roland Fuller/Dr. Arthur Grable)
  • Micole Mercurio (Mrs. Stodie)
  • Kerry Sandomirsky (Tracy)
  • James Sloyan (Dr. Frank Nollette)

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"

• Episode Number: 24
• Original Air Date: May 13, 1994
• Written by: Chris Carter
• Directed by: R.W. Goodwin
• Guest Cast:
  • William B. Davis (Smoking Man)
  • Anne De Salvo (Dr. Anne Carpenter)
  • Lindsey Ginter (Crew Cut Man)
  • Jerry Hardin (Deep Throat)
  • Ken Kramer (Dr. Terrance Allen Berube)
  • Jim Leard (Captain Roy Lacerio)

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.