1993 is a year in the 20th century.
- February 26: The World Trade Center is bombed by terrorists. Several people are killed and the building is damaged. Agent Marty Neill, an acquaintance of FBI agent Tom Colton, investigates the bombing for the government. (TXF: "Squeeze")
- March: Special Agent Dana Scully is assigned to the X-files Unit to debunk Special Agent Mulder's work. (TXF: Pilot)
- August 13: Luke Doggett is murdered in New York City. (TXF: "Release")
- December 5: Harry Cokely is released from Macalester Penitentiary. He begins residing in Gainesville, Nevada. (TXF: "Aubrey")
- Shaineh Berkowitz has a tubal ligation, which prevents her from becoming pregnant. (TXF: "The Post-Modern Prometheus")
- Special Agent Dana Scully receives a Georgetown parking permit. (TXF: "Milagro")
- Special Agent Raymond Crouch retires from the FBI after a 21-year career. (TXF: "Millennium")
Saturday, March 6
- In the Collum National Forest in Northwest Oregon, A young woman scrambles through a darkened forest at night. She sees an immense light grow over a nearby hill. A figure approaches from the light and stands over her. (TXF: "Pilot ")
Sunday, March 7
- The next morning, Detective Miles and Coroner John Truitti nspect the woman's corpse with a team of coroners. Truitt shows Detective Miles two small bumps on the woman's lower back. A trail of dried blood runs from the woman's nose to her mouth.
- Special Agent Dana Scully has a meeting in Chief Scott Blevins' office. Inside, Blevins questions her about her past work while a mysterious man smoking a cigarette silently watches. She learns she is being assigned to work with Fox Mulder on the X-files, a group of cases that involve paranormal or inexplicable phenomena.
- In the building's basement, Scully meets Mulder in his office, while The Smoking Man eavesdrops on the agents' first meeting. Mulder shows her several slides of Karen Swenson's dead body and reveals that a strange organic substance has been found near the two marks on the woman's back.
- Although Mulder seems to believe that the cases are somehow linked to aliens, Scully argues that science will uncover a more logical explanation. He states that he and Scully will leave to investigate the deaths early the next morning. (TXF: "Pilot ") (TXF: "Musings of a Cigarette Smoking Man ")
Monday, March 8
- On an airplane to Oregon, Mulder lies sprawled across a row of seats, with his eyes closed and headphones in his ears. Scully meanwhile looks at newspaper clippings about the dead teenagers. She focuses on the name "Dr. Nemman".
- In Bellefleur, Oregon, while driving, the car's radio powers up and the agents hear a high-pitched noise. Mulder stops the car and uses an aerosol from the luggage compartment to spray a large, red "X" on the road directly behind the vehicle. When he returns to the car, Mulder states that the incident was probably only trivial.
- When the agents arrive at their destination, they meet with John Truitt and an assistant coroner. At the grave site, they discuss Ray Soames, the third victim whose body they are exhuming. But the coffin rolls down a hill. Mulder opens the coffin to find a desiccated, mummified body lying inside. The corpse is definitely not human.
- Later that night, while examining the corpse, Scully determines that the body is mammalian - possibly an orangutan or chimpanzee. Excited that the body may have been alien in origin, Mulder asks Scully to conduct a complete analysis of the corpse. Scully, reluctantly agrees to comply with Mulder's request.
- Later, Scully finds a small metallic implant in the body's nasal cavity. Mulder knocks at her door she says she has identified the implant in Soames' nose yet, she replies negatively and bids Mulder goodnight. (TXF: "Pilot ")
Tuesday, March 9
- Mulder and Scully visit the psychiatric hospital where they meet two of Soames' former classmates, the comatose Billy Miles and the wheelchair-using Peggy O'Dell. Peggy suffers from a nosebleed during the agents' visit and is seen to bear marks similar to Swenson's.
- That night, Mulder and Scully investigate the forest; Scully discovers strange ash on the ground, However, a Detective Miles arrives and orders them to leave. Driving back to their motel, there is a blinding flash of light and the car loses power. Mulder realizes that nine minutes disappeared after the flash, a phenomenon reported by alien abductees.
- At the motel, Mulder tells her that his sister's disappearance when he was twelve tore his family apart. They receive an anonymous call telling them that Peggy has been killed in traffic while on foot. Visiting the scene, to find her body and no wheelchair. Later they find the motel on fire and their evidence destroyed. (TXF: "Pilot ")
Wednesday, March 10
- Very early in the morning, Mulder and Scully go to the cemetery but discover that the bodies of the other two victims have also been exhumed. Mulder suddenly realizes the killer's true identity - Billy Miles, the boy in the hospital.
- In an attempt to confirm or disprove their suspicions, Mulder and Scully return to the hospital where Billy Miles is undergoing treatment. Scully shows Mulder dirt on the soles of his feet. Taking a sample of the dirt. Scully claims to be certain that Billy was in the same forest as the victims and matches the strange earth she found in Collum National Forest earlier.
- When Mulder and Scully arrive at the edge of the forest, they notice Detective Miles' car. A distant scream draws them into the woods. Scully follows Mulder as they run toward the source of the noise, but is suddenly ambushed by Detective Miles and falls to the ground.
- Mulder and the detective witness Billy Miles lift Theresa Nemman in his arms, as light eventually engulfs them all, as Scully watches from a distance. After the light dissipates, Billy has no memory of his actions and is confused. The spots on his back are gone and he is no longer crippled. (TXF: "Pilot ")
Monday, March 22
- Billy Miles undergoes hypnosis performed by Heitz Werber. Mulder is in the room with him, while Scully watches from an anteroom through a one-way mirror. Division Chief Blevins, the Cigarette-Smoking Man and the third man are also in the anteroom. Billy Miles says, he and his friends were having a party in the woods when he first saw the bright light. It transported him to a location that he calls "the testing place," where a group told him to gather the others so they could do tests.
- In Blevins' office, Scully and the Division Chief discuss the case. Scully hands over the implant found in Ray Soames' coffin, which was not destroyed in the motel fire, a lab test conducted failed to identify the material.
- After she is dismissed from Blevins' office, Scully passes the Cigarette Smoking Man in the corridor outside. She pauses to watch him enter Blevins' office, before continuing on her way.
- Later, Scully lies awake in bed. She answers a phone call from Mulder, who tells her that a case file on Billy Miles has disappeared from the District Attorney's office in Raymon County, Oregon. Mulder wants to talk with her and Scully agrees that they will discuss their situation on the following day.
- In a storage room in the Pentagon, the Cigarette Smoking Man files away the implant in a box containing many others, surrounded by rows upon rows of shelves, all containing similar boxes. (TXF: "Pilot ")
- In the Air Base in Southwest Idaho, a unit of armed Military Police prepare to storm a house, Mrs. Anita Budahas, is told by the commanding officer that her husband has violated and stolen an armed military vehicle. After breaking into the house, Mrs. Budahas demands to speak to her husband, later found curled up in a corner of the bathroom shiverig, and covered with a skin irritation. (TXF: "Deep Throat ")
Wednesday, May 5
Thursday, May 6
Friday, May 7
Saturday, May 8
Sunday, May 9
- The quiet town near Fort Dix is rocked by brutal murders. Two military personnel are found dead in public places, with their throats viciously slit. However, one of an eyewitness account paints a strange picture of the crimes. The killer has the power to blend into their surroundings and is invisible to its victims before it kills.
- Mulder and Scully are called to investigate, although Mulder is initially skeptical that the case is an X-Files, he soon encounters a local woman who believes that a goblin stalks the woods and realizes that there is something very strange going on now. (TXF Novel: "Goblins")
Tuesday, July 20
- In Baltimore Maryland, At dusk, a businessman, George Usher, walks onto a street in Baltimore, Maryland and strolls to his car, unknowingly watched by a pair of menacing yellow eyes from within a storm drain.
- After George exits an elevator in an office building, the doors to the elevator open again, but the cabin is gone. The cables in the open shaft tremble as if they are being used for climbing. Usher makes a call to his wife and then leaves his office for a cup of coffee. The noises abruptly end as a large dent is smashed in the door. As Usher's coffee drips on the floor and he lies dead, the vent is screwed back in place. (TXF: "Squeeze ")
Wednesday, July 21
- FBI Agents Dana Scully and Tom Colton are having lunch together in a Washington, D.C. restaurant. Colton then starts to tell Scully about a case he has been assigned that involves a series of three victims, the latest being George Usher, who were each killed in a location where there were no obvious entry points and found with their lives missing.
- In Usher's office, Mulder discovers a bizarrely elongated fingerprint on the vent that opened during Usher's murder but Colton dismisses the possibility that anyone could have crawled through it.
Thursday, July 22
- In the X-files office, Mulder shows Scully fingerprints that tie the recent murders to a series of related murders reported in the X-file, the others having occurred in Powhatan Mill 1963 and 1933, as well as one taken in 1903 (when fingerprinting was still in its infancy). Mulder eventually suggests that they conduct their own investigation, separate from that of the Violent Crimes Section.
- Scully types up a psychological profile of the killer at night. (TXF: "Squeeze")
Friday, July 23
- Scully presents her report to the VCS agents. On her recommendation Agent Fuller, Colton's superior, organizes stakeouts of the crime scenes, as Scully believes the killer will return to one of them. Fuller suggests that Scully work overtime with his team.
- Alone in a car, Scully is on a stakeout in the parking garage of Usher's building when she is alerted by a faint banging noise. Mulder notices that something is moving inside an air shaft. A man crawls out of the chute. He is then arrested by Colton and other agents.
- A polygraph test is conducted on the Eugene Victor Tooms, an employee of the Baltimore Municipal Animal Control. Colton and Fuller, watching from an adjacent observation room with Scully and Mulder.
- Later, the examiner declares that, in her own opinion, Tooms passed the test. Scully maintains, in opposition to Colton and Fuller, that the alibi remains questionable. Mulder notices that Tooms clearly lied on the two Powhatan Mill questions; when the examiner begins to explain the reading. (TXF: "Squeeze")
Saturday, July 24
- Using a computer, Mulder digitally elongates Tooms' fingerprint until it matches those found at the crime scenes, definitive proof that Tooms was responsible for Usher's murder as well as the previous murders.
- Another businessman named Thomas Werner arrives home while Tooms watches from the darkness. Once Werner enters his house, Tooms climbs up the side of the building onto the roof, and attacks Werner from behind as the last remaining embers go out. (TXF: "Squeeze")
Sunday, July 25
- While Detective Johnson takes measurements of where Werner's body is in relation to objects in the room, Scully begins to read a profile of Mr. Werner but Mulder cuts her off, having already found another of Tooms' elongated fingerprints on the fireplace. Mulder also notes that something has been removed from the mantelpiece.
- Mulder is searching through old records with a microfiche projector, coming across a 1903 census record concerning Tooms, as Scully enters.
- The agents are largely unsuccessful in their search but, after they have plowed through the records, Scully informs Mulder that she has found the current address of the investigator of one of the murders in 1933. (TXF: "Squeeze")
Monday, July 26
- The agents visit the now-retired Frank Briggs at the Lynne Acres Retirement Home. He recounts how he, an experienced detective at the time, was appalled by the 1933 murders and experienced a sense of evil in the room at Powhattan Mill where they were committed. he shows the agents photographs that he himself took in 1933, including a picture of Tooms - in which he looks virtually identical to his current appearance.
- Mulder remarks, as he and Scully enter the bare apartment where the census record stated Tooms was living, that Briggs was right about there being a strong sensation. Mulder discovers a hole in the wall behind a propped-up mattress and the agents climb down into an old coal cellar.
- On their way out of the cellar, she becomes momentarily caught on something in the darkness and a hand, holding her necklace, reaches down from the rafters, where Tooms watches. (TXF: "Squeeze")
Tuesday, July 27
- Mulder is waiting outside Tooms' building at 66 Exeter Street when Agents Kennedy and Kramer arrive. Mulder reminds them of their objective, adding that he and Scully will relieve them in eight hours if Tooms does not make an appearance.
- At the FBI Bureau, Scully is preparing to meet Mulder when Colton bursts in. He voices his frustration with the fact that Scully is using two of his men and Scully is furious when Colton tells her that his regional ASAC called off the stakeout and tries to call Mulder with the news. Scully drives home and goes inside, not knowing that Tooms is watching her from the bushes across the street.
- Mulder drives up to Tooms' building and is surprised to find no-one no one waiting for him. He runs inside. In the cellar, Mulder discovers Scully's necklace amongst the collection of trophies and rushes out.
- Scully finishes running her bath and Tooms bursts out of the vent and is about to rip out Scully's liver when Mulder kicks the front door in and manages to handcuff one of Tooms' hands but is as Tooms gives up, that the killer will not be able to fill his quota this time. (TXF: "Squeeze")
Wednesday, July 28
- Detective Briggs is relieved to the point of tears when he sees a report about Tooms' capture in the Section Twonewspaper.
- Another copy of the same article is ripped up and licked by Tooms, who uses it towards building a new nest in the psych ward cell where he is now confined. Scully says official findings confirm that Tooms is genetically a human anomaly.
- The agents wander away as a food tray is brought to the cell and passed through a small, rectangular slot in the door. Alone in his cell, Tooms stares at the slot and smiles, sinisterly. (TXF: "Squeeze")
Saturday, August 7
- At night – in Campsite 53, beside Lake Okobogee – a family consisting of a teenage girl, a younger boy and their mother are sleeping, A violent shaking sends the mother falling to the floor while a bright light begins to shine into the RV from outside. Moments later, the light suddenly dissipates,. As the woman hears her young son, Kevin, screaming for his mother outside, Outside, a frowning Kevin immediately tells his mother that Ruby, his teenage sister, has disappeared. (TXF: "Conduit")
Monday, August 16
- Four months after the incident at the Air Base in Southwest Idaho, Mulder and Scully meet in a downtown Washington, D.C. bar at lunchtime. Mulder briefs Scully on the disappearance of Colonel Robert Budahas, the man found by the military police earlier; he is, since 1963, the sixth pilot to have gone missing from Ellens Air Base, where he had been stationed.
- In the bar's washroom, Mulder encounters the man who was watching him and Scully earlier. The man reluctantly introduces himself as a potential government informer and warns Mulder to stay away from the case, stating that the military will not tolerate an FBI investigation. Mulder tries to follow the man out of the washroom but loses track of him.
- At the FBI Headquarters, Scully researches Ellens Air Base in a library within FBI Headquarters, finding that the base is known for attracting UFO buffs.
- In his apartment, Mulder answers a call from Scully, in which she complains about her discoveries, but he notices that his telephone is apparently bugged and that someone is watching from a van parked outside. He refuses to discuss Scully's concerns with her until their flight and quickly hangs up. (TXF: "Deep Throat ")
Tuesday, August 17
- Arriving in Marriette Field. The agent's question Mrs. Budahas, She also tells Mulder that neighbor Verla McLennen's husband similarly went "kind of crazy. The agents confront Kissel outside his house, but he refuses to cooperate with them and demands that they leave. After he hurries inside, the agents are met by local journalist Paul Mossinger. He remarks on the abundance of "UFO nuts" in the area, seemed skeptical of the UFO phenomenon.
- At "The Flying Saucer" diner, Mulder and Scully meet a woman who identifies the noise of yet another speedy aircraft as an F-15 Eagle and remarks on the arrogance of the pilots.
- At night, Scully is asleep in the car as a low rumble begins to sound but she wakens with a start upon hearing the vehicle's rear window shatter. Mulder hurriedly returns to the car, eager to show her something. Mulder and Scully watch two strange lights in the sky.
- The FBI agents watch two strange lights dance above the base, theorizing about what they are. After the lights seemingly rise out of sight and collide, the agents notice an approaching helicopter and two teenagers, a girl, and boy, who are fleeing the base. (TXF: "Deep Throat ")
Wednesday, August 18
- In a roadside diner, the teenagers, Emil and Zoe recount their experiences at the base/ When Mulder shows Emil the picture he bought earlier, Emil claims it looks exactly like the craft he has seen,
- Mulder tries to convince Scully that there is a connection between the crafts at Ellens Air Base and the UFO that reportedly crashed in Roswell, New Mexico in 1947.
- Mulder and Scully continue to argue while driving along a highway, but are cut off and boxed in by two cars, out of which step several Men in Black. The men proceed to search the agents' car and confiscate all their evidence.
- In her motel room, Scully ends a phone conversation with a contact named Gail, finding that her attempt to track down one of the cars has been fruitless. Mulder eventually leaves for the Base against Scully's wishes.
- Emil and Zoe lead Mulder to a hole in the fence that surrounds Ellens Air Base. Mulder walks onto a runway, a triangular craft speeds towards him, instantly slowing to hover above him, and then shines a dazzlingly bright, white light down on him before darting away. Mulder is captured by army personnel.
- Still struggling inside one of the military vehicles, Mulder is injected with something and held down until he apparently loses consciousness. (TXF: "Deep Throat ")
Thursday, August 19
- Scully, meanwhile, struggles to make a phone call to Washington, D.C. Leaving her gun in her room, she goes to the motel manager and asks to use his phone, which also doesn't work. The Manager tells her that one of the nearby military interference is the fact that phones are pretty undependable in the area.
- The military vehicle carrying Mulder enters a hangar where Mulder's gurney is offloaded from the vehicle. As it is wheeled through the building he, in his drugged state, sees men working on a large, spaceship-shaped object that is obscured behind a large sheet of plastic.
- Scully is attacked by Paul Mossinger, Although Mossinger breaks into the car and tries to grab Scully, she manages to pull his own gun on him. Emil and Zoe arrive and Emil tells Scully that they took Mulder to the base.
- In a medical facility, a light is shone into Mulder's eye, into which is then dropped a driblet of a silver solution.
- Scully and Mossinger arrive at the base's entrance, where Scully exchanges Mossinger for Mulder. As they drive away, Scully asks Mulder if he's okay, but he can only respond with confusion as to how he got there.
- The agents visit the Budahas residence but Mrs. Budahas, noticeably discomforted, claims her husband is fine and quickly thanks the agents for their concern before shutting the door in their faces. Mulder is convinced the military have visited Mrs. Budahas and threatened her into keeping silent. (TXF: "Deep Throat ")
Monday, August 23
- In an office at FBI Headquarters, Scully types up her field report, in which she recounts that Colonel Budahas was returned home – albeit in a highly bewildered state – and refuses to confirm Mulder's theory that the colonel may have suffered stress-related trauma as a result of flying aircraft using recovered UFO technology. She officially closes the case.
- While jogging at a local race track, Mulder meets Deep Throat – the secretive man who approached him in the bar. The man warns that the agents' lives may be in danger, because they have seen things that were not meant to be seen. As Deep Throat starts to walk away but momentarily turns back when Mulder asks if aliens are indeed already on Earth. Deep Throat responds they have been on the planet for an extremely long time. (TXF: "Deep Throat")
Wednesday, August 25
- Chief Blevins informs Scully of a 302 that Blevins has indirectly received from Mulder. Blevins shows Scully case X-40253 – which concerns the disappearance of Mulder's sister, Samantha, an incident that happened years ago.
- In the basement office of the X-Files Unit, Scully challenges Mulder on the validity of his request. Mulder replies the disappearance occurred at Lake Okobogee, a known UFO Hotspot. He also lets Scully know that one of four well-documented UFO sightings from 1967 involved a young girl scout, now the missing girl's mother, Darlene Morris. (TXF: "Conduit")
Thursday, August 26
- The next day, Mulder and Scully arrive at the Morris residence in Sioux City, Iowa and are welcomed inside by Darlene, who tries to introduce them to Kevin but he ignores them, all the while scribbling something on paper. Darlene gives a statement to the agents, claiming she and Kevin have been traumatized by the loss of Ruby, such as Kevin has been acting strangely since the disappearance.
- Mulder tries to talk with Kevin but finds him busily watching static on the TV set and copying a binary string onto a pad of paper. Kevin insists the transmission is coming from the TV, even though Mulder observes only static.
- At the Sioux City Police station Mulder faxes Kevin's transmission fragment to Danny Bernstein at the FBI Cryptography Section. In a simultaneous telephone call Fox promises Danny tickets to a Redskins game as compensation for attempting to decipher the binary string.
- Mulder and Scully find a note stuck to their car and covertly meet a friend of Ruby's in a public library who claims that Ruby's boyfriend, Greg Randall, got her pregnant and that the two had been planning to leave town.
- Later that night, Mulder and Scully venture to the Pennsylvania Pub in search of Greg Randall who was apparently employed as a barman there. Mulder poses as a UFO skeptic, and pays off as the man shows the pair his right ear which is badly burnt and disfigured due to what he calls a "killer sunburn at night" at Lake Okobogee. (TXF: "Conduit")
Friday, August 27
- At 5:30 a.m. the next morning, agents from the NSA burst into Scully's hotel room demanding to know where Mulder is. Mulder is then quizzed by Agent Holtzman as to where he obtained the binary string he faxed the previous day which is revealed to be a defense satellite transmission.
- The Morris residence is ransacked by NSA Agents later that day, and Kevin's possessions are boxed up to be taken away for investigation, while many other items in the house are broken or damaged in casual disregard for the family's rights and freedoms.
- Darlene and Kevin Morris are roughly ejected from the NSA building, while Darlene explains that she wants nothing more to do with the FBI.
- Mulder explains to Scully that he believes Kevin has been touched by whatever abducted Ruby. Mulder discovers that the grave contains Greg Randall's body with a note inside his wallet (which still contains money) that reads: Dr. Jack Fowler Aug.7 - 2:30
- They match the hand-writing from this note to the one pinned to their car; both are written by the girl they met at the library whose name they discover to be Tessa.
- Scully argues that they should now hand the case over to local law enforcement and close the X-file, Mulder refuses and presses on to try to find Ruby. (TXF: "Conduit")
Saturday, August 28
- They return to the Morris house, which is empty, with the front door unlocked and many sheets of paper laid out on the lounge floor. The papers are covered in neatly written binary strings, Scully looks at the arrangement from the mezzanine level above the lounge and from this new perspective sees the chilling image of Ruby Morris' face made up from 1's and 0's.
- In the dark, the pair return to Campsite 53 and find the Morris' RV abandoned by the shore. They follow a trail into the forest and find Darlene trying to catch her breath
- Mulder finds Kevin walking towards a bright light which turns out to be the headlights from dozens of bikers off-roading through the forest. Mulder and Kevin run back when they hear Scully's screams to find an unconscious Ruby lying on the forest floor. (TXF: "Conduit")
Sunday, August 29
- At the Sioux City hospital, Scully and Mulder discuss the health of Ruby who has been awake for a few hours. She has several unusual symptoms that Mulder claims can be caused by prolonged weightlessness. When Mulder's desperate pleas to Darlene to let Ruby speak about her experiences again.
- Back in Washington, Scully reviews Mulder's hypnotic regression tape concerning his sister's disappearance. Mulder describes the room, his paralysis and his sister's cries for help as she was being abducted, at the same time the real Mulder sits in a church crying, looking at his sister's photo. (TXF: "Conduit")
- Despite the year provided for the Pilot onscreen, the end of Season 4, opening of Season 5, Season 9 and Season 10, as well as other evidence strongly suggests a 1993 start date to when Mulder and Scully first meet. Since Mulder and Scully act and behave as if they're new partners, the timeline indicates the 1992 date is incorrect.