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 While there, they encounter endless tricks and traps set by a ghostly couple who originally made a lovers suicide pact in the house.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.

A monster who feeds on human brain matter tries to lead a normal life, but he soon cannot control his feelings of hunger.

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.

Snakes are killing the unrighteous, but Mulder and Scully doubt that this is a case of divine intervention.

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.

Mulder and Scully suspect that hexcraft is the source of threats against a doctor's family.

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.

A series of coincidences leads Scully to a married man she had an affair with during medical school but left him to protect his family.

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.

A man whose blood is rapidly changing into metal alloy enacts revenge on those who caused his condition.

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.

Scully and Doggett must race against the clock to investigate and fight off a contagion lurking in the subway tunnels of Boston.

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.

Special Agent Reyes enlists Mulder's help in investigating a supernatural killer's connection to the unsolved murder of Agent Doggett's son, Luke.

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.