Agent Dana Scully is assigned to work with Agent Fox Mulder on the X-Files in an attempt to debunk his work on the paranormal. Their first case takes them to Oregon to investigate the unsolved murders of several high-school classmates.

Mulder and Scully 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 who claims to have classified information about investigations into the paranormal.

Mulder and Scully track a legendary creature that has roamed the New Jersey countryside for over forty years..

Mulder and Scully are contacted by a communications specialist from NASA who shows them evidence of sabotage in the space programme.

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.

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.

A young man who has the power to heal people with his touch begins to question his gift when people start dying after he has supposedly healed them.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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 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.

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.

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.

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 the attempted assassination of Corporal Frish.

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.

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.

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.

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 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.

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.

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.

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.

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 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.

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 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.

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 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 soldier and that the people she has killed were poisoning the water supply, and she wants Doggett to expose the truth.

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.

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.

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.

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.

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.

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.