Though X-Files has been shut down, reassigned Mulder investigates a a tip from his mentor, leading him to a communications center in Puerto Rico, looking for evidence of a close encounter.
Mulder is assigned a mysterious murder case in New Jersey, and Scully discovers a strange worm-like creature slithering inside the corpse.
When several violent deaths in a small farming community are connected to the destruction of digital devices, Mulder believes that people are being driven to kill by the use of subliminal messages in the digital readouts.
Mulder reluctantly accepts a new partner, Agent Alex Krycek, and they investigate the deaths of several Green Beret soldiers who participated in a sleep-deprivation experiment during the Vietnam War.
Mulder is called to a hostage situation involving Duane Barry, a former FBI Agent who claims to be an alien abductee and wants to get back to the abduction site with someone who will be taken instead of him. Unfortunately, the someone he chooses is Scully.
When Mulder finds out that Scully was kidnapped by Duane Barry, he risks the wrath of his superiors and the annoyance of Agent Krycek in order to do whatever it takes to find her. Meanwhile, Krycek is found to be reporting Mulder's activities to the CSM.
Mulder investigates a weird three-person cult, who kill in order to drink their victims' blood, believing it will make them immortal. He finds himself strangely drawn to a mysterious woman, who is linked to the three.
Scully mysteriously appears in a Washington hospital, alive but in a coma, and Mulder must fight to keep her alive in order to find out what happened to her and who did it. Meanwhile, Scully fights her own personal battle as she decides whether to stay or go on to the next world.
Mulder and Scully, reunited at last, head for an active volcano under a geological study and find a deadly life form that can survive in the searing heat of the crater, and is killing the scientists to avoid being discovered.
While investigating the connection between the abduction of several teenagers and a rural religious cult, Mulder and Scully discover the secret tests being performed on the children using the `Purity Control' alien DNA from `The Erlenmeyer Flask', which leads Mulder to the Crew-Cut Man, Deep Throat's murderer.
Mulder and Scully visit a nursing home to investigate a nurse's claim that she was attacked by supernatural forces while on duty.
Mulder and Scully investigate the possibility of transference of personality from one generation to the next, when a detective mysteriously uncovers the remains of an FBI agent who disappeared in the 1940s, while investigating a similar case to the one she is now investigating.
When Mulder and Scully investigate murders committed by a serial killer, Scully has to deal with her own demons brought on by the investigation.
2X14 - Die Hand Die Verletzt
The ritualistic murder of a teenager in a small town gets Mulder and Scully caught up in a secret occult practice within the local school's PTA, and a substitute teacher with strange powers.
Mulder and Scully investigate the deaths of soldiers, thought to be suicides, from a Haitian refugee camp in North Carolina.
Mulder and Scully investigate when an alien bounty hunter begins murdering doctors around the country without leaving traces of the bodies.
Mulder must find a way to capture an alien bounty hunter who has been murdering doctors and has kidnapped Scully.
When animals from a zoo in Fairfield, Idaho, disappear from their cages, reappearing miles away, and a local man is killed by an invisible force, Mulder and Scully investigate. They become caught in a conflict between an animal rights activist and a zoo director, and Scully is forced to conduct the strangest autopsy of her career.
Mulder and Scully investigate the rusting hulk of a new naval destroyer whose crew died of premature ageing. They are reminded of the Philadelphia Experiment, which took place during the Second World War where the US government attempted to make battleships invisible to radar, but stranded on the ghost ship, they also fall prey to a wrinkle in time.
Mulder and Scully travel to Gibsonton, Florida, a town built and populated by circus and sideshow performers, to investigate the death of Jerald Glazebrook, the Alligator Man. While searching for leads on the killer, the agents come across many bizarre characters including the local sheriff who was once known as Jim, the Dog-Faced Boy.
Mulder and Scully investigate a case involving a boy they believe was led to his death by an unseen force.
Scully quarantines a prison facility after a mysterious sickness proves lethal, killing a dozen men, while Mulder seeks two escapees.
During an investigation, Mulder and Scully discover a scientist at a chemical testing plant is missing following a freak accident.
A federal poultry inspector is killed by an axe-wielding masked man, but no body is found. During their investigation, Mulder and Scully discover an increasingly paranoid rural community uniting against them. Their first lead takes them to the Chako Chicken processing plant - where the agents rapidly lose their appetite.
A computer hacker's access to secret government files may threaten the lives of agents Mulder and Scully.