Agent Doggett investigates the death of an EPA official after his car is forced off a bridge by a woman he picked up. He asks for assistance on the case from Scully, who has returned to her teaching position at the FBI Academy in Quantico.
Mulder and Doggett join forces to investigate the arson attack on a genetics lab where one of the doctors suspected of experimenting with alien impregnation is killed. They encounter Billy Miles, who has been changed into an alien replicant after his recent abduction and is attempting to erase evidence of the tests; part of the Syndicate's conspiracy with an alien race. When a woman helping Scully out at home is found to be a part of the conspiracy, the agents, along with Monica Reyes and Alex Krycek, know they must protect Scully and her baby from Billy Miles and get her out of the city.
With otherworldly factions in pursuit, Mulder and the agents race to safeguard the birth of Scully's child. Scully and Reyes take refuge in an abandoned town where Doggett grew up. Meanwhile Doggett and Skinner have the final showdown with Alex Krycek and continue to fight off the replicates but how successful will they be?
After Agent Mulder goes beyond his jurisdiction to shine light on a possible X-file, Doggett is assigned to investigate the mysterious disappearance of two men aboard an oil rig. Once he arrives, he finds Mulder has taken it upon himself to start his own investigation. Mulder soon becomes convinced that the rig is drilling the black oil. Doggett and Mulder must attempt to stop the spread of the alien virus while avoiding the infected crew.
Scully is approached by a couple who claim their baby has the same abilities as William and have information about the super soldier program. Scully is forced into an awkward situation when she has to decide whether to put Mulder's life in more danger even though she desperately wants to see him.
When Teresa Hoese, the woman Scully & Mulder met the previous spring in Oregon just before Mulder was abducted, is found in a desert, returned from testing done on her by aliens, Doggett alerts Scully that this could have something to do with Mulder and his whereabouts.
Shortly after Mulder is buried, Billy Miles is found very dead but somehow comes back to life. Skinner and Scully put all their hopes into digging up Mulder and discovering that he too, is still alive. As Mulder lies in hospital without indication that he is going to fully recover, Krycek comes to Skinner and offers him a vaccine to the virus that has infected Mulder - but the cost of the vaccine is that Skinner has to kill Scully's unborn child.
When Scully and Doggett are contacted by a man who claims his wife was murdered shortly after giving birth to an alien baby, Scully digs deeper into reports of alien fertilization on humans and begins to question her own pregnancy and its conception.
Mulder's request for reassignment to the X-Files is denied by Kersh, who hopes that Mulder will simply quit the FBI. When a census worker is killed on the White House lawn trying to get information to the President, Mulder gets in over his head trying to discover what the man knew.
Newly appointed Deputy Director Kersh organizes a manhunt for Mulder and assigns Agent John Doggett to head the team. Scully and Skinner go along with the investigation but are warned by Kersh that they will be fired if anything is said about aliens. Scully , along with the Lone Gunmen, surmise that the Bounty Hunter is trying to erase all evidence of abductions and they realize that he may be going after Gibson Praise, who is now living at a school in Arizona. Agent Doggett comes to the same conclusion and his team race Scully and Skinner to the school where they find Mulder trying to kidnap Gibson.
As the search for Mulder intensifies in the Arizona desert, Gibson Praise leads Scully to believe that she is truly closer to her target. Meanwhile AD Kersh informs Agent Doggett that he has been assigned as Mulder's successor on the X-Files.
Mulder and Scully return to the town of their first X-Files investigation where a UFO has crashed in the forest. CSM arranges for Krycek to be released from prison in order for him to make contact with the aliens and begin rebuilding the 'Project', while Scully's health appears to be taking a turn.
Scully evades Doggett's help in investigating a vicious murder in a remote area of Utah and she is trapped in the small town by a religious cult that believe a slug-like creature is the second coming of God who needs a human host to survive.
A Los Angeles police officer who is being filmed for the show COPS is attacked by a strange monster and Mulder and Scully are investigating the case. Scully is wary of having their faces put on national television but Mulder welcomes the publicity.
After the miraculous recovery of a young boy who had cancer, Mulder and Scully investigate what has happened but Scully is shocked when The Smoking Man tells her that he cured the boy and offers to show Scully the cure for cancer if she travels with him. But hides her trip from Mulder.
A young girl disappears from her home and Mulder requests the case even though it is a full FBI matter, not just an X-File. When Mulder takes some outrageous leaps to convince the girl's parents that she will be found, Scully fears that Mulder is becoming too personally involved with the case because of his sister's abduction.
After arresting the murderer of Amber-Lynn LaPierre and discovering a mass grave site containing the bodies of dozens of missing children, a man comes to Mulder and claims to have had visions of other victims who aren't buried at the site. Despite Scully's objections, he takes Mulder on a journey which reveals what truly happened to his sister.
Mulder and Scully are caught in a real-life Rube Goldberg device as they investigate a man cursed with extremely good luck since he survived a plane crash back in 1989. The man, Henry Weems, insists that he is never unlucky but he finds out that he cannot pass on his good luck to others without severe consequences to their part.
A series of prison breaks bring Agents Mulder and Scully face to face with Scully's former kidnapper, Donnie Pfaster, as Scully is forced to question her faith and confront the clash of morality and religion. But Scully soon learns that Donnie is very keen on going after the one victim that managed to escape him, Dana Scully when Reverend Orison breaks him out of prison
While Scully travels to Africa to piece together the meaning of the symbols on the spaceship beached on the Ivory Coast, Mulder is imprisoned by his own frenetic brain activity. He manages to get a message to Skinner who finds Kritschgau and together they try to understand what is happening to Mulder before it is too late.
Scully frantically searches for a way to help her ailing partner without having anyone to turn to for help, while a catatonic Mulder's dreams lead him away from his mission and the X-Files to a place which he believes is a better life.
While on a stakeout of a Government Defense Convention in Las Vegas, The Lone Gunmen are reunited with Susanne Modeski, the mysterious woman who disappeared at a Convention ten years earlier when they first met Agent Mulder.
Two scientists confer about each of their metal objects that were found in Africa and they theorize that the objects are pieces of a puzzle which could be undeniable proof that human, plant and animal life did not originate on this planet. When one of the scientists is killed and the objects are stolen, the agents investigate and Mulder begins to experience severe neurological pain caused by the objects.
A writer living next to Mulder becomes obsessed with Scully and confesses to her that he is using her for a character in his novel. Scully finds herself strangely drawn to him even though he is now the prime suspect in the murder case that she and Mulder are investigating.
Mulder meets with Agent Arthur Dales' brother (also named Arthur!) and is told a tale of a talented negro baseball player from Roswell, New Mexico in the 1940's who may have been an alien that ran away from his colony because of his love for the game.
A woman is forced to relive the same day over and over as she tries to prevent Mulder and Scully from being killed by her boyfriend during a bank robbery attempt; and as the events restart again and again, Mulder's sense of deja-vu grows stronger.
On their first official case back on the X-Files, Mulder and Scully go undercover as a married couple at a prestigious planned community where several residents have recently disappeared after failing to comply with the rules and regulations.
While Cigarette Smoking Man recites to an unseen listener everything about the work of the Syndicate involving a global conspiracy in co-operation with an alien species, Cassandra Spender reappears and is pursued by the scientists who would rather kill her than keep her alive.
CSM reveals all the government secrets from the past 50 years in order for his son, Jeffery Spender, to join him in his work. Mulder learns that the final stage of the conspiracy will soon begin with the hybridization of the Syndicate members and he must stop it from happening. Agent Spender deceives his father and arranges for Mulder and Scully to be reassigned to the X-Files, which doesn't sit too well with CSM.
While being detained near the famed "Dreamland" Area 51, a strange craft flies overhead and Mulder swaps bodies with an Area 51 'Man-in-Black'. While the other agent has fun in Mulder's body, Mulder himself finds it difficult to fit into someone else's life, especially a shadowy one.
Mulder is thrown in jail at the Area 51 compound but is released when it is discovered that the flight data recorder he stole was a fake. Scully comes to her senses and realizes that the Mulder she sees isn't who he really is and heads back to Nevada to help the real Mulder. Meanwhile, the mechanism that caused the body swap is rapidly snapping back, undoing everything in it's wake and Mulder and his alter ego must race to put themselves back where they belong.
Mulder and Scully have 24 hours to save Assistant Director Skinner from being killed by a biologically engineered disease. The disease appears to be created by a shadowy government organisation but in order to save Skinner's life; they must determine who wants him dead, and why. With Skinner's condition worsening Mulder seeks assistance from Senator Matheson who he hopes can provide some answers and help him to find a cure.
Cigarette Smoking Man returns as Mulder investigates the attempted assassination of a young boy with psychic powers who may be the proof that he has looked for all his life. On his way he encounters many enemies especially in the finale' as his office and every X-File is torched by CSM.
Mulder is less than thrilled when an Office of Professional Conduct board refuses to reassign him and Scully to The X-Files and even more so when he learns that Agent Spender and Agent Fowley have become their successors. When Gibson Praise reappears and comes to them for help, Mulder and Scully attempt to continue their quest undercover despite having fewer friends and less access and protection than ever before.
Mulder and Scully meet Cassandra Spender, a woman who claims to be a multiple abductee and wants to deliver a positive message about the aliens. Mulder who now is skeptical of extraterrestrial activity and believes that the government is behind the abduction phenomena is disturbed when Scully forms a special bond with the woman. A series of group attacks against abductees take place and the shadowy Syndicate believes that a rebel alien resistance is attempting to destroy all their work.
After the gathering at the abduction site where everyone is killed by the rebel bounty hunters, Cassandra Spender disappears and Mulder is blamed by her son, Jeffrey, who is an up-and-coming FBI agent and opposed to Mulder's work. Meanwhile, the Syndicate are continuing their tests to create a vaccine for the Black Cancer and Marita Covarrubias becomes an unwilling test subject.
After Mulder chases down and kills a young man whom he believes to be a vampire, Scully realizes that his fangs are fake. The agents then return to DC, aware of the mistake they just made. Faced with a lawsuit from the family of the man, they recount each of their sides to the story leading up to the event.
Agent Fox Mulder visits an aging FBI Agent Arthur Dales and listens to a story of the agents assigned to a would-be X-File in the Cold War era of the 1950's and how Mulder's father was connected to a series of strange deaths.
Filmed in glorious black and white with a comic book feel to it, this is a modern retelling of Frankenstein as Mulder and Scully get caught up in a town where the residents live on Jerry Springer episodes and fear a two-faced monster who has been impregnating the women.
Master of Horror Stephen King's first effort at an X-File sees Scully's well deserved vacation going terribly wrong and landing her in a small Maine town where one of the residents is believed to be a witch and her autistic daughter's doll has frighteningly evil powers.
Scully fights to protect her daughter's life, while Mulder discovers her true origins.
As Mulder continues his search for a cure for Scully’s illness—and the identity of a mole operating from within the Bureau—he receives help from a most unlikely source.
In 1989, the Lone Gunmen meet for the very first time when they assist a woman who claims the government plans to use civilians as guinea pigs in a secret experiment.
Mulder and Scully search for the truth when an anthropologist discovers what could be the frozen remains of extraterrestrial life.
While celebrating Scully's birthday, Mulder learns of Max Fenig's death in a plane crash. What the agents soon discover is that the circumstances surrounding the crash may have been alien.
As the investigation into the crash of a commercial airliner continues...Mulder is placed under military arrest after he discovers the existence of a UFO crash site. Scully mourns the loss of a fellow agent.
A headless corpse walks out of a hospital morgue—triggering the search for a highly-evolved humanoid life form that possesses unimaginable regenerative powers.
A diplomatic courier carrying deadly cargo involves Agents Mulder and Scully in a dangerous web of intrigue, which leads Mulder on a trip to Russia.
An incarcerated serial killer claims Mulder’s sister was one of his many victims.
Scully recounts the investigation of an alleged UFO encounter for a famous author researching his latest novel.
Pursued by an Alien Bounty Hunter, Jeremiah Smith takes Mulder to a farm where he finds several girls who are clones of his sister.
The agents play a deadly game of cat-and-mouse with a killer who can control people’s minds.
An “alien autopsy” videotape and a Japanese diplomat’s murder spark Mulder’s search for a strange creature aboard a train. Scully encounters a group of people who reveal information about her disappearance.
When Mulder becomes trapped aboard a train rigged with an explosive device, Scully searches for the truth behind the government’s involvement with secret experiments.
The agents investigate the deaths of several young people who were apparently struck by lightning in the same small town.
As Scully faces possible dismissal from the F.B.I., a manhunt ensues for the missing Agent Mulder.
As Mulder searches for a killer capable of altering his shape, a woman who claims to be his long-lost sister suddenly appears.
The agents investigate a murder in a small town populated by devil worshipers.
Scully and Mulder hunt down a fetishist who collects pieces of the dead.
A former FBI agent who claims he was abducted by aliens takes several people hostage.
Mulder attempts to rescue Scully after she is abducted by a strange man who believes in UFOs.
Mulder pursues a humanoid, parasitic organism that uses sewage systems as its home.
Mulder searches for a Vietnam veteran who can project his consciousness into other people's minds.
Scully believes that the psychic predictions of a death row inmate are the only hope of apprehending a vicious murderer.
Mulder and Scully are sent to investigate when a team of geophysicists stationed at a remote Alaskan outpost is killed by a parasitic alien life form.
Mulder becomes obsessed with solving a case that closely parallels an encounter he experienced as a child.
Agent Dana Scully is instructed to debunk an FBI project dubbed "The X-Files" cases linked to the paranormal that have been reopened by Agent Fox Mulder.
Mulder and Scully investigate the strange disappearance of Lieutenant Colonel Robert Budahas, a test pilot for the military who experienced a psychotic episode and was supposedly hospitalized for treatment. Mulder suspects that Budahas may have met the same fate as six other pilots who mysteriously vanished from Ellens Air Base while participating in experimental aircraft test flights. He hints to Scully that the disappearance may be linked to the paranormal— classifying it as an “X-File” case.