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There is no Next Episode of The X-Files planned.
With the X-Files closed, Scully has been assigned as an instructor at the FBI Academy while Mulder is doing menial surveillance work. After meeting with Senator Matheson, one of his supporters in regards to The X-Files, Mulder disobeys orders and heads to an abandoned SETI site in Puerto Rico which has unexplainably reactivated itself and could provide proof of contact with extra-terrestrial life.
AD Skinner sends Mulder to investigate a body which washed into the New Jersey sewer from the ocean. Mulder believes that the basic blue-collar assignment is punishment, but on Skinner's own admission what he discovers is a true X-File.
When several violent deaths in a small farming community are connected by 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 requests a strange case because someone put an audio tape in his morning paper. When his request is granted they investigate the deaths of several Green Beret soldiers who participated in a sleep deprivation experiment during the Vietnam war. But before long it becomes clear that not one of these men have slept in over 20 years.
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 eventually 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.
Truly alone for the first time since Scully found her way to the basement of the J. Edger Hoover Building, Mulder throws himself into his work, and into the bizarre world of vampire-fetishist in search of a trio of serial killers. But Mulder finds himself falling for the one woman that may be the prime suspect.
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 to her. 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 & Scully discover a secret test 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 investigate when the rape and battery of a nurse takes place in a Massachusetts convalescent home. The nurse claims that she was attacked by one of the residents but also claims they were invisible. Mulder and Scully soon discover that it may not be one of the residents after all...
When a detective mysteriously uncovers the remains of an FBI agent who disappeared in the 1940s while investigating a murder case similar to a modern-day one she is investigating, Mulder and Scully believe that the original killer had passed his genetic trait of violence to his grandchild.
A mortuary worker, who gets his thrills from collecting hair and fingernails from the dead, begins killing people to expand his collection and sets his seriously disturbed sights on Scully.
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.
While investigating several deaths and murders within a Haitian refugee camp, Mulder and Scully get caught in the middle of a secret war between the camp commander and a Voodoo priest.
After the obituaries of three identical men are e-mailed to Mulder, the agents are contacted by a CIA agent who tells them about a Russian Spy Killer sent to eliminate evidence of Cold War era Russian clones who had infiltrated the American medical establishment.
The alien bounty hunter kidnaps Scully and wants to trade her for Mulder's sister, who is revealed to be a clone herself. After the trade goes badly and Mulder discovers the truth about Samantha, he tracks the bounty hunter to his ship buried in the arctic ice and demands the whereabouts of his real sister.
Invisible animals are rampaging through town, destroying property and trampling a federal employee. On arriving in town, the agents begin their search at a nearby zoo with the distinction of never being the site of live birth. Whether that's because as Mulder suspects, Aliens are 'harvesting'' the young or, as Scully insists, an animal rights group determination to close down the zoo, the only reliable witness appears to be a hand-signing gorilla named Sophie.
When half the crew of a Navy ship abandon their boat in a life raft and are rescued 18 hours later looking about 60 years older than they should be, Mulder suggests that the ship is caught in a time field which is speeding up their aging.
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 Jim, the Dog-Faced Boy.
A balloon traveling into the face of the wind isn't much of a clue to launch an investigation into a toddler's death, but, on their arrival, a series of bizarre events convinces Scully they're dealing with a rare form of child abuse. For his part, Mulder thinks answers may be found with a pair of dead roosters and a group of elderly chanters called the Calusari.
When a plaguelike illness kills 10 men inside a maximum security prison, Scully tries to get into the quarantine site and discover the cause and origin of the contagion, while Mulder and a group of US Marshals track two escapees who may be infected.
When people start disappearing, and the case is shoved in her general direction, Detective Kelly Ryan, one of Scully's former students, turns to her old teacher for assistance. Mulder's theories, in fact his very presence, become more and more un-welcome as the body count continues to mount in his general vicinity. Mulder's growing disinclination to share his thoughts on the case in the face of Ryan's- and Scully's!-evident skepticism doesn't endear him to the woman, either.
After several disappearances in a small town, Mulder and Scully investigate and find hundreds of human bones in the river and discover that the man behind the town's main source of wealth, a chicken processing plant, has found a way to prolong his life through cannibalism.
Mulder obtains what could be the original and uncut MJ documents containing information about the government's knowledge of extraterrestrial life, which could lead him closer to the truth than ever before. But Mulder's enemies make sure he learns that there's a heavy price to pay for his much sought after truth.