Little Green Men

With the X-Files shut down, Mulder secretly journeys to a possible alien contact site in Puerto Rico while Scully tries to help him escape detection.  First appearance of Senator Matheson.  

The Host

Mulder stumbles upon a genetic mutation, nicknamed the Flukeman, while investigating a murder in the New Jersey sewer system.  X makes his first appearance, via phone.

Blood

Several residents of a small suburban community suddenly turn violent and dangerous, prompted by digital readouts in appliances urging them to kill.

Sleepless

Mulder is assigned a new partner, Alex Krycek, and they investigate a secret Vietnam-era experiment on sleep deprivation that is having deadly effects on surviving participants.  X appears in person.  1st appearance of Alex Krycek.

Duane Barry (part 1)

Mulder negotiates a hostage situation involving a potentially dangerous and psychotic man, Duane Barry, who claims to be the victim of alien experimentation.

Ascension (part 2)

Mulder pursues Duane Barry in a desperate search for Scully who has been abducted. 

3

Mulder investigates a series of vampiresque murders in Hollywood and finds himself falling for a mysterious woman who is a prime suspect.

One Breath

Scully is found alive but in a coma, and Mulder must fight to save her life.  1st appearance of Melissa Scully.

Firewalker

Mulder and Scully stumble upon a deadly life-form while investigating the death of a scientist studying an active volcano.

Red Museum

Mulder and Scully investigate a possible connection between a rural religious cult and the disappearance of several teenagers.

Excelsis Dei

Mulder and Scully uncover strange goings-on in a nursing home after a nurse is raped by an unseen force.

Aubrey

Mulder and Scully investigate the possibility of genetic transferring of personality from one generation to another in connection with a serial killer.

Irresistible

A death fetishist who collects hair and fingernails from the dead steps up his obsession to killing his soon-to-be collectibles himself.  Profoundly disturbed by the case, Scully returns to Washington to do research and discusses her fears with a counselor.  Upon returning to Minneapolis, Scully is kidnapped by the chilling psychopath.

Die Hand Die Verletzt

Mulder and Scully journey to a small town to investigate a boy's murder and are caught between the town's secret occult religion and a woman with strange powers.

Fresh Bones

Mulder and Scully journey to a Haitian refugee camp after a series of deaths, finding themselves caught in a secret war between the camp commander and a Voodoo priest.

Colony (part 1)

Mulder and Scully track an alien bounty hunter who is killing medical doctors who have something strange in common: they are all clones.  Mulder is soon summoned to a family emergency to discover that sister Samantha has returned.  Samantha identifies the bounty hunter as a shape-shifter, and Scully, investigating on her own, is pursued by him. Mulder to First appearance of the alien bounty hunter.  First appearance of Mulder's mother and father (Bill Mulder).

Endgame (part 2)

Mulder tracks an alien bounty hunter who has taken Scully prisoner while discovering that his sister may not be who she seems.  Mulder soon discovers the ruse, that he was manipulated by the Samantha clones and doctor clones to protect them and their unsanctioned work from the aliens who've dispatched a bounty hunter to dispose of them, and departs for the arctic to track down the bounty hunter.   The bounty hunter tells Mulder his real sister is still alive and leaves him to perish in the Arctic.  Scully, desperate to find Mulder, contacts Skinner and X.  The two men have a physical confrontation, but Mulder's whereabouts are discovered in time for Scully to rescue him

Fearful Symmetry

Mulder and Scully investigate animal abductions from a zoo near a known UFO hot spot.

Død Kalm

Mulder and Scully fall victim to a mysterious force aboard a navy destroyer that causes rapid aging.

Humbug

Mulder and Scully investigate the bizarre death of a retired escape artist in a town populated by former circus and sideshow acts.

The Calusari

A young boy's unusual death leads Mulder and Scully to a superstitious old woman and her grandson, who may be possessed by evil.

F. Emasculata

When a plague-like illness kills 10 men inside a prison facility, Scully is called to the quarantine area while Mulder tracks to escapees who may be carrying the plague.

Soft Light

An experiment in dark matter turns a scientist's shadow into a form of instant death.

Our Town

Mulder and Scully investigate a murder in a small Southern town and its strange secrets surrounding a chicken processing plant.

Anasazi (part 1)

Mulder and Scully's lives are jeopardized when an amateur computer hacker gains access to top-secret government files providing evidence of UFO's.  Mulder's father is fatally shot in his home by Krycek to prevent him from telling Mulder anything.  Scully discovers Mulder's water has been drugged and finds Mulder about to shoot Krycek.  To prevent him from committing murder, she shoots him in the shoulder and secrets him away to New Mexico, where Albert Hosteen, a Native American translator is decoding the files.  Mulder recovers and is lead to a hidden underground boxcar where the bodies of experimented alien/human hybrids are discovered.