Mulder is arrested for investigating the plane crash and interfering with a military operation, while Scully is caught in an attempted assassination of Corporal Frish which claims the life of Agent Pendrell. Scully bails Mulder out of prison, and they go to Max Fenig’s trailer to find out why he was on the plane. Mulder finds evidence of alien technology and boards a plane with it, but the plane is intercepted mid-flight and it disappears. Mulder is again left with nothing.
45 minS1:E1
Pilot
The agents' first case takes them to Oregon to investigate the unsolved murders of several high-school classmates.
Mulder and Scully head to Ellens Air Force Base to investigate the mysterious case of a military test pilot who disappeared after experiencing strange psychotic behavior. While on the case, Mulder meets a mysterious man dubbed 'Deep Throat' who claims to have classified information about his investigations into the paranormal.
As Section Chief Blevins expresses his concern with the direction of the X-Files, Mulder becomes obsessed with solving a case that closely parallels an encounter he experienced as a child: the abduction of his kid sister, Samantha.
Mulder puts the future of the X-Files in jeopardy when he heads to a UFO crash site being rapidly covered up by the military. He is arrested, and while in jail he meets Max Fenig, a UFO nut whose NICAP group has followed Mulder's work on the X-Files. When Mulder is released, Scully urges him to return to Washington to face his superiors and try to save his job, but Mulder finds out that Max is more than meets the eye and ignores Scully to try and save him instead.
When two fathers on opposite sides of the country are inexplicably murdered at the exact same time in the exact same way, Mulder and Scully are called in to investigate. When they discover that the two fathers' eight-year-old daughters are identical twins, they realize that something even stranger is going on.
An old Oxford girlfriend of Mulder's asks for his help on an international case concerning the unexplainable execution of several British dignitaries, and they encounter an assassin who can produce fire from his bare hands.
When death row inmate Luther Lee Boggs claims to be psychic and can lead Mulder to a serial killer in return for a lesser sentence of life in prison, Scully becomes an unwilling believer when Boggs tells her that she can communicate through him with her recently deceased father.
A series of sexually-oriented murders, which are identical except that the killer appears to be both male and female, draws Scully and Mulder to an Amish-type community of people called the Kindred.
When FBI Agent Jack Willis and bank robber Warren Dupre are both shot at the same time during a robbery attempt, Dupre dies when Willis is brought back to life. When Willis rushes out of the hospital and begins acting strangely, Mulder concludes that Dupre has come back to life in Willis' body.
Mulder becomes the target of someone from his past named John Barnett. He was a jewelry store robber with an itchy trigger finger that Mulder sent to prison when he first joined the Bureau. The only problem is that Barnett died four years ago.
Mulder and Scully receive information from Deep Throat about a UFO that was shot down over Iraq and has been secretly transported to the US. However, Deep Throat then intentionally misleads the agents to prevent them from discovering the truth.
Mulder and Scully travel to a Native American reservation to investigate the death of a man who was mistaken for a wild animal and may have been the legendary Manitou, a man who can shape-shift into a beast.
When a group of loggers in the Washington State National Forest disappear in the same way that another group disappeared 50 years ago, Mulder and Scully go along to investigate and find themselves trapped in a cabin surrounded by flesh eating insects that only attack at night.
Eugene Tooms is released from the sanitarium, and Mulder becomes personally involved to ensure that he is caught in the act of getting the last human liver he needs to go into hibernation for another 30 years.
After a detective and his former partner die in unexplained circumstances, the accidents are linked to a little girl who witnessed both deaths. Mulder believes that she may be the reincarnation of a policeman murdered by his colleagues.
Mulder and Scully investigate the death of a scientist working on advanced propulsion technology. The mentally challenged janitor Roland, who has secretly been completing the scientist's work, is the prime suspect.
When Deep Throat points out a news story about a fugitive who apparently drowned, Mulder and Scully cannot see what makes the case special but follow it up anyway. With Deep Throat's insistence, they discover evidence of a secret government project code-named Purity Control, which uses human test subjects and infects them with extraterrestrial DNA. However, the evidence and everyone who has seen it is quickly being eliminated.
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 inexplicably reactivated itself and could provide proof of contact with extra-terrestrial life.
A.D. 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 by 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 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 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 Cigarette-Smoking Man.
Mulder, back on the X-Files but alone for the first time, investigates a series of vampire-like murders in Los Angeles and 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 and 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 uncover strange occurrences in an elderly care home when one of the nurses is attacked by an unseen force she claims to be one of the 90 year old residents.
When a detective mysteriously uncovers the remains of an FBI agent who disappeared in the 1940s while investigating a similar murder case to one she is now on, 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 his soon-to-be collectibles himself 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 four identical men are e-mailed to Mulder, the agents are contacted by a shadowy CIA agent who tells them about a bounty hunter sent to wipe out the beginning of a colony of clones. Meanwhile Mulder is distracted by the sudden reappearance of his sister Samantha.
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.
In a small town in Idaho, a man is killed by what seems to be an invisible elephant. Mulder's investigation into the local zoo, its owners and a local animal rights group uncovers evidence of insidious alien experiments.
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.
When a plague-like illness kills ten 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.
An experiment in dark matter accidentally turns a scientist's shadow into a deadly weapon that can unzip a person's molecules if they are touched by it.
After several disappearances in a small town, Mulder and Scully investigate and find hundreds of human bones in the river. They 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 receives an encrypted computer disk containing the defense department's top secret files on extraterrestrial life and becomes a target. Scully takes him to a Navajo family that unearthed a buried secret to decipher the disk.
Scully finds her career with the FBI in jeopardy as Mulder is still missing and the Cigarette Smoking Man is pursuing the stolen files. The Navajo elders find Mulder's body in a cave and perform an ancient ceremony to call the spirit back to the empty vessel.
A.D. Skinner and Scully are at a standoff when Mulder bursts in and discovers that Skinner has the digital tape. Reunited, Mulder and Scully travel to a secret vault inside a mine and find an elaborate filing system of medical records which reveals that Mulder's sister may not have been the first choice for abduction. Meanwhile, Skinner deals with the Cigarette-Smoking Man for their safety.
Mulder and Scully investigate a series of human and cattle deaths by lightning and are led to a teenage boy who is the only survivor out of five people recently hit by lightning strikes.
In the midst of a psychic sideshow while on a murder case, Mulder and Scully enlist the help of a man who may have a true psychic ability to foresee how people will die to help the agents catch a man killing fortune tellers.
Nobody takes much notice when a death row inmate vows on the electric chair to come back from the dead and kill five men who have wronged him during his time in prison, until a guard is mysteriously murdered in the former inmate's cell.
A man with a genetic abnormality who must prey on overweight women in order to suck the fatty tissue from their bodies, begins to meet his victims through internet chat rooms.
After a suicide attempt and multiple murders at a military hospital, Mulder and Scully meet a quadruple amputee who has gained the power of astral projection and is taking out his personal frustrations on his commanding officers.
Mulder seeks the help of a woman who he believes has a special connection with a young girl who has recently been kidnapped by the same man who held her captive many years earlier.
An investigation into a video of an alien autopsy puts Mulder and Scully in the middle of a conspiracy involving WWII Japanese scientists brought to America to continue their experiments which may shed light on Scully's abduction.
Mulder is trapped inside a train car which contains a suspected alien-human hybrid and also a bomb, while Scully pursues the truth about her abduction and the mystery behind the implant in her neck.
Mulder and Scully swap roles as they pursue a man killing priests that claim to have the wounds of Christ. The agents find and must protect a young boy who may be a real stigmatic. While Scully's faith draws her close to the boy, Mulder is convinced of another explanation.
Widespread panic is caused in a small community after numerous deaths are linked to killer cockroaches, and a government agricultural agency is discovered to have set up a secret experiment involving insects.
A rare planetary alignment causes strange behavior in the residents of a small town, but particularly in two teenage girls who were born at the exact same moment on that date. While investigating the strange occurrences Mulder's interest in the local female detective makes Scully jealous.
A serial killer is captured after a three year manhunt, and he claims an evil spirit is responsible for the crimes. When the killings continue as he sits in jail, Mulder's battle with a former colleague gets more heated when he suggests that something more paranormal may be involved.
A French salvage ship searching for a lost WWII fighter plane unknowingly surfaces an alien which appears in the form of black oil and has the ability to jump hosts. Mulder heads to Hong Kong to investigate the salvage broker who sold the information to the French and he encounters Krycek, who has been selling information from the MJ documents. As Mulder prepares to take Krycek back to the US, the alien makes its way to Hong Kong and takes control of Krycek.
Mulder pursues Krycek (unaware of the alien that has taken over his body) to get back the DAT tape containing the MJ documents. Meanwhile, the shooting of A.D. Skinner uncovers evidence that could lead Scully to her sister's murderer.
Mulder and Scully are asked to help in a case involving Robert Patrick Modell, a murderer possessing the psychic ability to force his will onto people. Due to a brain tumor that is slowly killing him, he is searching for a "worthy adversary" and forces Mulder into a battle of mind over matter.
The unearthing of an ancient Ecuadorian Amaru urn and its removal to America despite protests leads to a series of deaths linked to a shaman spirit released by the urn.
Mulder, Scully and a local Chinese American cop investigate deaths of several Chinese men found to be missing vital internal organs. The clues lead them to a deadly secret lottery run by the Triads in San Francisco's Chinatown district. The game is free to play but losing will cost you more than an arm and a leg.
A alien abduction of two teenagers with endless versions of the same story prompts a science-fiction novelist to to write a book about the incident; however, nobody involved with the investigation can tell him the full story with any accuracy.
During a one-night-stand in the midst of his divorce, A.D. Skinner becomes a murder suspect, and Mulder and Scully return the many favors that he has done for them by analyzing evidence that someone doesn't want uncovered to prove his innocence.
Mulder and Scully investigate a series of disappearances and attacks around a lake where Mulder believes that the local legend about a lake monster may be all too real. Frustrated Scully insightfully confronts Mulder about the futility of their work on the X-Files.
Mulder and Scully investigate a series of murders linked to a mysterious device that alters television signals causing paranoid hallucinations. One of them falls victim to it.
After his mother suffers a stroke under strange circumstances, Mulder searches for a strange, benevolent alien man that possesses miraculous healing powers. With the help from Mr. X, he learns about the involvement of the Cigarette-Smoking Man and uncovers some secrets kept by his parents.
With his mother on a deathbed and the alien bounty hunter in pursuit, Mulder decides to put Jeremiah Smith, the alien healer, in mortal danger for a chance to finally uncover the whole truth behind the alien conspiracy. Meanwhile, the Syndicate suspects that they have a traitor in their midst and set up a trap.
A baby is found buried alive in shallow ground and appears to have birth defects resulting from generations of inbreeding, leading Mulder and Scully to a reclusive family who have a history of inbred children.
After several African-American men are killed and the color is drained from their skin, Mulder learns about the Teliko, an African folktale about a creature who must suck the pigmentation from a persons body in order to survive.
Several kidnappings of young women linked by distorted photographs lead Mulder and Scully to a man who can imprint his darkest fantasies onto undeveloped film and is trying to save the women from the "howlers".
After an FBI raid on a doomsday cult called the "Temple of the Seven Stars", Mulder meets Melissa, a cultist who claims to have known him in a previous life during the American Civil War. Scully believes the woman is a delusional schizophrenic, but Mulder allows himself to be drawn into her fantasies.
After a doctor loses control and kills a patient on the operating table, Scully hypothesizes that it's linked to work-related stress, while Mulder is convinced of a more sinister reason. After he finds a link between the victim and the four witches Sabbaths, he suspects that a nurse may be practicing witchcraft.
The Lone Gunmen reveal the (possibly fake) secret history of the Cigarette Smoking Man to Mulder and Scully; from a young captain in the U.S. Army recruited to assassinate President Kennedy, to becoming the mysterious man in the shadows at the height of a global conspiracy.
Mulder is given a tip about potentially dangerous paramilitary operations on the U.S. soil but during the sting operation is surprised to find out the identity of his mysterious informant - it turns out to be Alex Krycek. Suspicious about his true motives, Mulder reluctantly follows the information provided by Krycek. However, soon he discovers a much bigger conspiracy which takes him to a gulag in Tunguska, Russia where prisoners are being used for experiments involving a substance of alien origin.
While imprisoned in Russia and infected with the Black Cancer, Mulder learns that Krycek is working with the men responsible and everything has been a setup from the start, while Scully and Skinner are called to a suspicious Senate hearing where the only question is the whereabouts of Agent Mulder.
Mulder's dreams help him in finding the body of a little girl which reopens one of his old cases in the Violent Crimes Unit. This leads him to believe that the killer he captured had more victims and that Mulder's sister Samantha may have been one of them.
After a strange yellow rain kills a migrant girl, her family believes that a mythical creature el chupacabra was the cause and that it has manifested itself inside her fiancé's brother, who has since disappeared.
After the body of a decapitated EMT disappears from the morgue and an identical man starts work at the same hospital, Mulder believes that the man has the ability to regrow parts of his body, including his head. The agents soon discover that Betts' body is riddled with cancer and he is able to live in that condition but needs to feed on cancerous tumors to keep up his strength.
While Mulder is forced to take a vacation he leaves Scully with an assignment to keep her busy until he returns. However, she decides to start living and goes on a date with a man who believes that his tattoo talks to him and is telling him to stay away from other women.
Scully's recent failing health is revealed to be an inoperable cancer in her skull, which appears to be common among abductees and she attempts to come to terms with her condition. Meanwhile, Mulder and the Lone Gunmen break into a high-security research lab to find the cure that could save her life.
After a Jewish man is murdered in a Jewish community, his killers are murdered, too. Mulder and Scully have to determine whether someone is exacting vengeance or larger forces are at work.
When a U.S. military general is inexplicably murdered in the back of his limousine, a paramilitary group is suspected. They believe it was a soldier who they liberated from a Vietnam POW camp and is plotting to kill certain corrupt military figures.
While celebrating Scully's 33rd birthday, a strange woman informs Mulder that NICAP member Max Fenig (see Fallen Angel) has recently died in a plane crash. After a visit to the crash site and finding Max's body with radiation burns on it, Mulder suggests that the plane was intercepted by a UFO and is rapidly being covered up by the military.
Mulder is arrested for investigating the plane crash and interfering with a military operation, while Scully is caught in an attempted assassination of Corporal Frish which claims the life of Agent Pendrell. Scully bails Mulder out of prison, and they go to Max Fenig's trailer to find out why he was on the plane. Mulder finds evidence of alien technology and boards a plane with it, but the plane is intercepted mid-flight and it disappears. Mulder is again left with nothing.
A case involving a strange old man warning two scientists of events in the immediate future which come to pass (and the use of their experimental flash-freezing compound that does not exist yet) has Mulder believing that one of the scientists has come from the future to stop his own scientific breakthrough from becoming reality.
Five babies in the same town are all born with tails and the local OB-GYN is blamed for tampering with fertilized eggs. However, Mulder discovers the culprit to be a simple man with a genetic deformity who may have the ability to alter his appearance.
After a swarm of bees mysteriously kill a postal worker in an enclosed restroom, Assistant Director Skinner covers it up by destroying the evidence. In order to complete the task he poses as Agent Mulder, however his deception backfires. When Mulder finds out and confronts him, Skinner reveals that he is working for the Cigarette-Smoking Man in order to obtain a possible cure for Scully's cancer.
After a man sees a woman trapped inside a bowling alley pin setter, he goes for help and finds police standing next to a body of the same woman. Mulder and Scully join the investigation and follow up this lead which the police won't bother with, and they are led to a mentally challenged man who works at the bowling alley.
Covered in blood and suffering from amnesia, Mulder pieces together the events of the last few days, but the trail leads to a double murder that appears to have been committed with Mulder's weapon.
Mulder fights to prove that a discovery frozen in the mountains of Canada is an irrefutable evidence of alien life, but his quest for the truth only leads to more lies and an unthinkable conclusion.
Scully helps Mulder fake his own death in order for him to go undetected through the Department of Defence and find out the answers to his new questions about the government hoax concerning the existence of extraterrestrial life. Meanwhile, at a joint FBI/DOD inquiry, Scully's attempt to drive out the Conspiracy's informant is halted as her cancer takes a bad turn.
The Cigarette-Smoking Man helps Mulder to obtain Scully's cure and also lets him see his real sister who doesn't turn out to be as happy to see Mulder as he would've liked. In return for this, the Cigarette-Smoking Man asks that Mulder quit the FBI and work for him in the Syndicate where he could have power and respect which Mulder turns down, deciding to stay on the side of justice. While Scully's cure appears to have worked, the Cigarette-Smoking Man faces his own enemies and disappears, presumed dead.
Set in 1989, the story of the founding of The Lone Gunmen is finally told as we see how a straight-laced federal employee, a sex mad AV expert, and a nerdy computer hacker meet Susanne Modeski, a strange woman with evidence of a government conspiracy. When their plan to expose the conspiracy fails and Susanne is captured by a group of men-in-black, led by none other than X, they soon become a paranoid group of government watchdogs.
While on their way to an FBI group communication seminar, Mulder and Scully manage to escape when they come across a situation in the Florida forest area where three men have recently disappeared.
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.
On her Christmas vacation with her brother's family, Scully receives a mysterious phone call from a familiar voice who says, "She needs your help. Go to her." The phone call leads Scully to a murder case where the victim's 3-year-old adopted daughter bears an uncanny likeness to her sister, Melissa, at that age. The emotional roller coaster that follows has Scully believing that her sister had a baby during a period when she traveled the country and she tries to adopt the child, knowing that caring for the little girl would change her life.
DNA testing on Emily reveals that she is actually Scully's daughter and Mulder comes to assist her and to find out where and how the girl was born while Scully tries to help Emily with her own serious illness, a rare form of anemia.
Pusher returns as Robert Patrick Modell escapes from the mental hospital and the FBI promptly organizes a manhunt, assuming that he will continue where he left off. But is he really trying to get revenge on Mulder, or does he want to warn him of another evil?
A therapist working with children from abusive families is found to be implanting them with the memories of her own abuse suffered at the hands of her late father, when one of her patients tries to kill his stepfather.
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.
A super-intelligent virus program is let loose on the internet and begins to grow and expand by itself, eventually killing its creator when he tries to eradicate it.
After Mulder chases down and kills a young man who he believes to be a vampire, the agents 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. In the extremely humorous stories that follow we see how Scully and Mulder both perceive each other.
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's new found disbelief in extraterrestrial activity is enhanced while 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. Meanwhile, the Syndicate is continuing their tests to create a vaccine for the Black Cancer and Marita Covarrubias becomes an unwilling test subject.
In 1990 Agent Fox Mulder visits an aging FBI Agent named Arthur Dales. He 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.
Mulder and Scully try to get answers out of a stubborn blind woman found at a murder scene who may have the ability to look through the killer's eyes in her mind.
Scully faces her Catholic faith and the loss of her daughter Emily when she is asked to help a family whose adopted daughter was found dead in a position that looked like she was struck down by God himself.
Scully fears that Mulder has gone to the other side when she sees him assisting a federal suspect escape custody. In truth he has infiltrated a terrorist group testing a deadly biological weapon that can eat through a person's flesh.
Mulder is held hostage inside an office where a man claims his boss is a monster and has clouded all their minds while he turns them into zombies one by one, which is disbelieved until Mulder opens his mind and allows himself to see it too.
The 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.
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 is trapped in a car with a man who has developed a serious ear condition which can only be suppressed by driving west at high speeds. As Scully tries to find the cause and a cure for the problem, Mulder and the man get closer and closer to the ocean.
Mulder goes to the Bermuda Triangle when he learns that the Queen Anne, a British luxury liner which disappeared during WWII, has reappeared in the middle of the Sargasso Sea. Mulder's boat is wrecked and after floating in the water, he is hauled aboard the ship which has just been hijacked by the Nazis searching for the man who will build the atom bomb.
Mulder tries to convince the crew that they have traveled into the future, but evidence further suggests that it is he who is back in the past.
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 contacts Scully about the body swap and tries to get her the flight data recorder from the UFO test flight, but his alter ego uses Mulder's FBI persona to have him arrested.
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 its wake, and Mulder and his alter ego must race to put themselves back where they belong.
Mulder talks Scully into investigating a haunted house on Christmas Eve where several couples have met their fate on that very night. While there, they encounter endless tricks and traps set by a ghostly couple who originally made a lovers suicide pact in the house. The ghosts try to convince Mulder and Scully to kill each other.
After a scan of a couple's unborn child is found to have strange growths protruding from the head and back, the fetus is taken from inside the mother by a demon creature while she is asleep. Mulder heads to investigate after Agent Spender dismisses the claims, and discovers that the father is actually a demon who wants to have a normal child.
Strange weather phenomena in a small town leads Mulder to believe that a weatherman's deep emotions and unspoken love toward his workmate are becoming real in the form of snow and tornadoes.
Mulder and Scully have 24 hours to save A.D. Skinner from being killed by a biologically engineered disease. The disease appears to be created by a shadowy government organization, 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.
Assistant Director Kersh tries to tear Scully and Mulder apart when he partners Scully with a New York agent investigating Alfred Fellig, a freelance police photographer who conveniently shows up to document the scene of a death as soon as it happens.
While the young hotshot agent is convinced that Fellig is murdering the people, Scully has other (paranormal) theories.
While the Cigarette-Smoking Man recites to an unseen listener everything about the work of the Syndicate involving a global conspiracy in cooperation with an alien species, Cassandra Spender reappears and is pursued by the scientists who would rather kill her than keep her alive. Cassandra runs to Mulder's apartment and demands that he shoot her because she is the culmination of 50 years work - a living alien/human hybrid - and colonization will begin if the aliens find out about her.
The Cigarette-Smoking Man 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 the Cigarette-Smoking Man.
Arthur Dales summons Mulder and Scully to his holiday home in Florida where he is concerned over the disappearance of his neighbors. Despite the raging hurricane, Mulder and Scully head out to investigate and discover several strange deaths caused by an octopus-like sea creature that swam in through the overflowing sewer system.
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. 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.
A mysterious dog thought to be the last of a rare Asian breed is responsible for several murders which Mulder and Scully are investigating. Now the agents have to find a way to stop the dog before it kills again.
After a tornado rips through a prison camp, one of the inmates disappears from solitary confinement and the prison warden is killed. As Mulder and Scully track him, he appears to have the power to pass through solid matter while changing its composition.
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.
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 ten years earlier when they first met Agent Mulder.
When the bodies of a couple who have been missing for less than a week are discovered to have been reduced to bone, Mulder suggests that recent paranormal phenomena in the area may have caused the accelerated decomposition.
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.
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.
As the year 2000 draws closer, the agents are up against a man from the Millennium Group who believes that he can bring about the end of the world on the 31st of December if he resurrects four former members from the dead. To gain more insight into the group and its practices, Mulder and Scully enlist criminal profiler Frank Black to assist them in the investigation.
A young man who has gained the ability to move faster than the eye can see begins to use his new power to kill his enemies, including the local sheriff who happens to be his father.
Mulder and Scully get caught in a real-life Rube Goldberg device when they meet Henry Weems, who just may be the luckiest man on Earth - except everyone around him doesn't seem to be that lucky.
Reverend Orison hopes to save Donnie Pfaster's soul by helping him break out of prison, but Donnie immediately plans to go after the victim that once escaped him... Scully.
When a small-time magician performs a trick where it appears that he turns his head all the way around but is then found in his van dead with his head neatly sawed off, Mulder and Scully suspect he was murdered and get caught up in an intricate scheme planned by two magicians trying to rob a bank.
A young girl inexplicably 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.
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.
The Lone Gunmen call Mulder and Scully to a virtual reality development lab where they learn that one of the program testers was killed inside the computer generated game environment by the digital image of a woman. Needing to get his yah-yah's, Mulder enters the game to fight the woman, but Scully must step in to save him.
The Cigarette-Smoking Man offers to show Scully the cure for all diseases if she travels with him, but on one condition: Mulder must not know about her trip.
As Mulder investigates a missing person case with a key feature being a menacing raven, he learns to enjoy the creature comforts of a well-tended home while Scully must tough it out on an uncomfortable stakeout.
While protecting a man due to testify against the Morley cigarette company, Skinner is horrified when the witness dies mysteriously. What the agents soon discover is that a new brand of cigarette has a dangerous secret.
Mulder and Scully watch a movie with themselves as characters and are thoroughly disgusted at how they and their case are portrayed on the big screen. They recount how 18 months earlier they were followed around by a Hollywood producer while investigating a case concerning The Lazarus Bowl - a mythical piece of pottery reputed to have inscribed on it the words that Jesus Christ spoke when he raised Lazarus from the dead.
Mulder and Scully cross paths with two women who are identical and have followed each other across 17 states in the last three years, causing chaos and mayhem wherever they are.
Mulder and Scully discover a genie in a rug who, after 500 years of granting wishes, has come to the conclusion that people are still as greedy and self-centered as they always have been, and she begins to corrupt the wishes she grants if they are not specific enough.
Mulder and Scully return to the town of their first X-Files investigation where a UFO has crashed in the forest. The Cigarette-Smoking Man 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.
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, A.D. Kersh informs Agent Doggett that he has been assigned as Mulder's successor on the X-Files.
While tackling his first X-File case about a series of gruesome murders surrounding a bat-like creature, Doggett quickly learns that his investigative techniques are somewhat dissimilar to Scully's.
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.
In 1990 a little boy inexplicably disappeared from his crowded school playground and was never seen again until now, ten years later, and he hasn't aged a day.
A prominent lawyer wakes to find himself in jail and about to be prosecuted for the murder of his wife. He has no memory of this event however, and when the days begin to regress backward towards the murder, he realizes that he has been given a second chance.
Working without Scully's input, Doggett and Skinner try to stop the mysterious murder spree of a drug-induced religious cult leader, and it becomes clear that the man can enter the dreams of the people he knows and can kill them in their sleep.
When a real estate agent is shot inside a prison cell by someone who apparently fired from the roof, Scully and Doggett track him to two exterminators, one of whom has x-ray vision.
An Indian mystic whose son died in a chemical plant accident smuggles himself into the United States and takes his revenge on two families in suburban Washington, D.C.
Doggett comes upon an old case that Mulder kept secret from Scully and he follows up the investigation, hoping to find a possible connection to Mulder's disappearance.
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 she begins to question her own pregnancy and its conception.
When Teresa Hoese (the woman Scully and Mulder met the previous spring in Oregon just before Mulder was abducted) is found in a desert after enduring alien testing, Doggett alerts Scully that this could have something to do with Mulder and his whereabouts. Skinner joins them and they travel to the hospital where Teresa is clinging to life by a thread, and Scully realizes that this is exactly what's going on with Mulder.
Shortly after Mulder is buried, Billy Miles is found very dead, but he 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 the 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.
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.
Mulder and Doggett are reluctantly thrown together to investigate several deaths aboard an oil rig, and Mulder becomes convinced that the rig is really carrying the black oil alien.
While Scully takes maternity leave, Doggett is partnered with a young agent who is fascinated with the X-Files and has followed Mulder and Scully's careers. She and Doggett investigate the death of an old man and the disappearance of his son, but when they disappear as well Mulder heads out to search for them.
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. 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.
Mulder, Doggett and Skinner attempt to fight off the alien replicants, and they find a connection to the conspiracy that leads into the FBI while Reyes and Scully head to a remote farm to safeguard the birth of Scully's child.
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.
Doggett catches up with Shannon McMahon, the woman who the EPA official picked up. She claims to be a super solider and that the people she has killed were poisoning the water supply, and she wants Doggett to expose the truth.
Doggett and Reyes investigate the murder of a couple in West Virginia that has all the signs of a satanic ritual killing. They link the murder to a doctor who is incarcerated in a mental institute, and Doggett becomes convinced that the doctor is orchestrating the crimes from within the hospital.
During a stakeout of murderer Irwin Lukesh, Doggett sees Reyes attacked by Lukesh, but then we see Reyes and Doggett in her apartment, apparently both fine. Elsewhere at the same time, Doggett is shot and Lukesh identifies Reyes as the shooter. While Reyes is asked for her badge and gun by A.D. Follmer, and Doggett lies in hospital near death, the conflicting circumstances of the stakeout and Doggett's shooting do not add up and it becomes clear that Lukesh possesses the power to switch between parallel universes and alter the events in each.
When a stunt on a local cable reality show goes horribly wrong resulting in a man's death, Doggett and Reyes investigate. But when flies pour out of the victims eye sockets, they find themselves relying on Scully's expertise and ask her to join the investigation.
Scully is approached by a couple who claim their baby has the same abilities as William and have information about the super soldier program; however, they will only talk to Mulder, believing him the only person who can make the connections and uncover the truth. 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.
Scully and Reyes join forces to try and find Doggett when he goes missing. Doggett has his own problems, having woken up in jail in Mexico suffering from amnesia. With no knowledge of who he is, Doggett is befriended by a local who soon has him working smuggling illegal immigrants across the border.
Agent Reyes takes the lead while investigating an X-file case, surrounding a man found skinned alive after having visions of seeing other people appearing skinned alive. Reyes calls on Scully's expertise to help on the investigation, which pays off when Scully finds a link to a case from 1960.
When pieces of the spaceship beached in Africa resurface, the conspiracy within the FBI attempts to hide the information from the X-Files, especially the one person for whom the pieces have a special significance - Scully. When Doggett and Reyes discover that Scully and her child have been put in great danger, they race to protect her and William from the evil forces pursuing him, and Scully is forced to take drastic measures to protect her child.
Scully is anxious to recover William from his kidnappers and takes matters into her own hands when the FBI's attempts to assist in the investigation are less than helpful. With the help of the Lone Gunmen, Scully discovers terrifying information about her child's captors, and is once again forced to confront the mystery regarding the sinister interest in her son.
After a car accident, Reyes finds herself in a very gray area, while Doggett desperately denies doctors' diagnoses about his partner, who witnesses a strange disappearance.
Scully, Doggett and Reyes investigate an old case that Doggett worked on as a cop in Brooklyn, dubbed "The Screwdriver Killer". They try to determine whether the man who was convicted and has just been released from prison was actually the man responsible for the murders.
When Reyes uses numerology to connect the murders of several women to an obsessed serial killer, she and Scully become trapped with a mysterious checker-playing man who may or may not be the killer.
Agent Harrison talks Doggett and Reyes into investigating a boy's claim that monsters killed his mother, who was officially determined to have stabbed herself repeatedly.
The agents ask the Lone Gunmen to help find their friendly foe Yves Adele Harlow after former Area 51 Man-In-Black Morris Fletcher claims she is one of the super-soldiers.
Doggett catches someone in the X-files office trying to steal documents pertaining to Mulder's sister. The intruder is a severely scarred man who blames his disfigurement on Government conspirators. He claims the source of that information - and, in fact, the one who helped him gain entry - is Mulder. Although he refuses to divulge the missing agent's whereabouts, the mystery man has enough knowledge of the X-files and its history to lead Doggett to suspect that he just might be Mulder himself. Scully's fears for the safety of her son are elevated when he is injected with an unknown substance. With the mystery surrounding William becoming even darker, Scully must allow herself to send him away for his own safety.
When an FBI cadet with amazing profiling skills approaches Doggett, Reyes, and Scully with a lead on a suspect in a series of recent murders, he claims the same killer is responsible for the death of Doggett's son. The agents find themselves wondering if his knowledge of the deaths is because of his obsession with the cases he has studied at Quantico, or if he is in some way involved in the murders.
Doggett and Reyes investigate a murder outside the house that the original Brady Bunch series was filmed in. The house is owned by a man named Oliver who is obsessed with the show and has rigged the house into a series of traps and changing appearances to look like the Brady house.
After not knowing Fox Mulder's whereabouts for the last year, A.D. Skinner and Agent Scully learn he's being held for the murder of a military man he couldn't possibly have killed: Knowle Rohrer, one of the government's secret super-soldiers. With Skinner acting as Mulder's defense, people who Mulder has dealt with during his last nine years as an FBI agent testify on his behalf. But the military tribunal isn't interested in the truth.
When an unexpected person comes to Mulder's rescue, Mulder refuses to slip north over the border to safety. Instead, he heads southwest to the Anasazi ruins of New Mexico seeking a mysterious wise man who the Indians call "The Keeper of the Truth".
Agents Mulder and Scully return after 13 years to investigate a government conspiracy at the behest of a popular web-TV-show host, who introduces them to a woman who claims she's an alien abductee and shares startling news with them.
When Mulder and Scully try to discover what unseen force may have driven a scientist to commit suicide, they turn up a laboratory where extreme genetic experimentation has bred subjects possessing dangerous powers.
Mulder and Scully investigate a dead body in the woods, and try to determine whether it was the work of a serial killer, an animal or a mysterious creature seen by eyewitnesses. Meanwhile, a disillusioned Mulder confronts some of his own demons.
Mulder and Scully investigate the murder of a city official, a crime that doesn't appear to have been committed by human hands. Meanwhile, Scully faces deeply emotional feelings about the child she gave up for adoption.
Scully and Mulder investigate when an art gallery displaying offensive artwork is bombed, and need to discover a way to communicate with the comatose perpetrator to try and prevent a future attack.
The season concludes with people all across the country falling gravely ill. A widespread panic develops and Scully looks within to find a cure. Meanwhile, Mulder confronts the man he believes to be behind it all, but another figure from Mulder and Scully's past may prove to be the key to their salvation.
Mulder and Scully learn that they aren't the only ones desperately searching for their long-lost son, William. The very fate of the world may depend on it.
Exploring the idea of The Mandela Effect, in which large groups of people remember an alternate history, Mulder and Scully find out how the X-Files themselves may really have originated.
When a pair of teenage girls attack one another, each believing the other to be a monster, Mulder and Scully find that their investigation could possibly lead back to their long-lost son, William.
