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- Mulder accesses a facility that may hold a cure for Scully's illness. Scully performs an experiment in hopes of determining the origin of the disease.
- Scully is hospitalized after collapsing, while Mulder receives help from a most unlikely source as he continues to search for a cure for Scully's illness.
- In May 1989, the Lone Gunmen meet for the first time when they assist a woman who claims the government plans to use civilians in a secret experiment.
- In the unexplored woods of Florida's Apalachicola National Forest, Mulder and Scully investigate the disappearances of two land surveyors and a boy's claims that he and his father were attacked by an invisible creature.
- in this surreal, comical take on Frankenstein, Mulder and Scully arrive in a small rural town to investigate claims of a monster obsessed with Cher that's sedating and impregnating the local women.
- While visiting family for Christmas, Scully receives a mysterious phone call that leads to a woman's apparent suicide and a young girl who may be her sister Melissa's daughter.
- Scully and Mulder search for a cure to Emily's strange illness.
- Robert Patrick Modell, aka "Pusher," has recovered from his injuries and escaped from a prison hospital. Mulder and Scully lead the manhunt even as Modell may be using his powerful mind-control capabilities to target Fox for revenge.
- A teenager becomes the prime suspect in his stepfather's odd murder. Mulder is not buying it since the man was literally swallowed by the ground. After another parent is killed, the suspicion falls on someone close to the kids.
- Rumors of witchcraft and sorcery surrounding a bizarre murder at a supermarket in a small New England fishing town lead Scully, who's on vacation, to a little girl and a cursed doll that may be hiding a murderous presence.
- The brutal murder of a renowned computer programmer leads Mulder and Scully to investigate an artificial intelligence program loose on the Internet that has begun evolving on its own.
- Scully and Mulder each recount their version of events that led Mulder to drive a stake through the heart of a Texas teenager he claims was a vampire.
- Mulder and Scully search for answers when separate groups of alien abductees are burned alive. They meet a woman with an implant in her neck and symptoms similar to Scully.
- Scully undergoes hypnosis to recall her experiences on the bridge where the group of abductees was burned alive. Krycek provides the consortium with a vaccine for the black oil and tells Mulder of the planned colonization and alien rebels.
- In 1990, Mulder investigates the death of a man who disappeared in 1952 before he could be charged in a series of bizarre killings. The retired agent who worked the 1952 case recounts the facts to Mulder and the connection to his father.
- The prime suspect in a murder case is a woman who has been blind since birth, leading Mulder and Scully to conclude she may possess the ability to see through a killer's eyes.
- When a girl dies a mysterious death, Scully and Mulder discover more girls' lives are at stake in a divine battle of good versus evil.
- Mulder goes undercover to infiltrate a militia group armed with a deadly pathogen and wanted for domestic terrorism. Scully becomes suspicious when Mulder lets a suspect escape but she learns that his assignment may be a suicide mission.
- Paranoid telemarketer takes his coworkers and Mulder hostage claiming that their boss is a disguised insectoid monster that's literally turning the workers one by one into his zombie drones.
- A government assassin is caught trying to kill child chess prodigy Gibson Praise during an international chess tournament. Mulder's old flame Agent Diana Fowley arrives to help on the case but Scully is suspicious of her.
- After the events of The X Files (1998) movie, Mulder and Scully's new boss, Kersh, assigns agents Spender and Fowley to work on the X-Files instead of them. Ignoring this, Mulder takes Scully on a hunt for a rampaging alien.
- A man tormented by a piercing sound that could make his head explode unless he heads west as fast as possible takes Mulder hostage to drive for him, while Scully rushes to find the cause of this affliction that also killed the man's wife.
- Mulder boards the wreck of a legendary missing WWII ship that suddenly appeared in the Bermuda Triangle. The ship turns out to be a time portal. Now Scully must use all of her wits to try and get the unwilling FBI to help her save him.
- An anonymous tip finally brings Mulder and Scully to the mecca of all UFO lore, Area 51. But when the agents witness the flight of a mysterious craft there, Mulder and one of the Men in Black, Fletcher, somehow switch bodies - and lives.
- Scully begins to suspect that her partner's strange behavior is more than it appears to be, while Mulder fights to return his life to normal before it's too late.
- On Christmas Eve, Mulder and Scully find themselves trapped in a haunted house with two ghosts who are determined to prove just how lonely the holiday can be.
- A pregnant woman's baby is snatched away from her belly by a devil. Agent Spender believes the case is a joke, but Mulder decides to look into it on his own anyway. His investigation focuses on the woman's husband.
- When Mulder and Scully investigate a man who claims he can control the rain in a small, drought-stricken Kansas town, they encounter a force more powerful than the weather.
- When Skinner is infected with an unknown disease and receives a mysterious phone call telling him he has 24 hours to live, Scully and Mulder rush to find a cure and those responsible.
- A rookie agent asks for Scully's help in proving that a quaint crime scene photographer is a serial killer. With some help from a bored Mulder, Scully discovers the man's actual dark secret. And an old prophecy regarding Scully comes true.
- The alien rebels return to kill abductees including Scully and Cassandra Spender. With the Syndicate in shambles, the Cigarette Smoking Man reveals the truth to Agent Spender hoping that he will continue his work.
- Everyone prepares in their own way for the alien rebels' bloody endgame after which nothing will ever be the same again. Mulder and Scully try their best to stop the bloodshed and save Spender's mother.
- As a hurricane bears down on the Florida coast, the agents search for a sea monster that Arthur Dales believes is responsible for the disappearance of a couple and their son.
- A woman desperately attempts to change the outcome of the events of a day she is forced to relive again and again in which her boyfriend explodes a bomb during a failed bank robbery killing everyone inside, including Mulder and Scully.
- On their first assignment after being reinstated to the X-Files, Scully and Mulder go undercover as husband and wife in a high-class planned community where several couples have gone missing.
- A series of murders is blamed on a mythical Asian dog that supposedly escaped from the US cryptozoologist who caught it. Mulder asks a reclusive female dog expert for help which angers Scully. The woman leaves him a special gift.
- An escaped convict seems to have gained the ability to pass through solid objects as well as people. Mulder and Scully must find the deadly convict before he can get to his ex-girlfriend.
- A strange writer infatuated with Scully moves in next door to Mulder and proceeds to slowly bewitch her through his writing. Mulder investigates the man and realizes that he may be behind a series of killings involving psychic surgery.
- Searching through an FBI reference book, Mulder finds a photograph of Arthur Dales with a baseball team and the alien bounty hunter. Mulder goes to Arthur Dales' house to ask him about the photograph. There he finds Arthur Dales' brother, also named Arthur. Mr. Dales proceeds to tell Mulder a story of a 1940s Negro baseball player in Roswell named Josh Exley who was closing in on breaking some professional baseball records. Mr. Dales tells how he was assigned to protect this player from the KKK and that Exley was actually an alien.
- While infiltrating a defense contractor conference in Las Vegas, The Lone Gunmen are reunited with Susanne Modeski, the mysterious woman who disappeared 10 years earlier after the trio first came together to help her.
- The skeletal remains of a young couple are found after they have been missing for only three days in an area known for UFO activity. Mulder and Scully have different experiences in the investigation but nothing is quite as it seems.
- Mulder believes metallic objects discovered on the coast of West Africa are proof of the extraterrestrial origin of life on Earth. He falls mentally ill under the apparent influence of the artifact while Scully goes to Africa for answers.
- Scully and a colleague try to decipher the symbols on the spaceship beached in Africa before their rival can take over the dig, but the ship starts recreating the Plagues of Egypt. Skinner and Kritschgau test Mulder's telepathic ability.
- 1993–201845mTV-147.7 (3.3K)TV EpisodeScully searches for Mulder after the Cigarette Smoking Man takes him from the hospital for unknown purposes. An unconscious Mulder dreams of a better life away from his mission and the X-Files. But perhaps he is being led astray.
- Rob Roberts has an addiction to human brains. As he tries to control this overpowering hunger and turn his life around, Mulder and Scully try to find out who the brain-eating monster is.
- In this backdoor series finale to Millennium (1996), Mulder and Scully ask Frank Black to help them prevent a zombie apocalypse orchestrated by the rogue members of the now disbanded Millennium Group on the very eve of the new millennium.
- A high school boy is accused of the violent murder of a sheriff's deputy. Mulder believes he is innocent. The agents find that someone with super-human speed may be the culprit.
- A man is tossed off the top of a 29 story building by gangsters. Amazingly, he gets up and walks away unscathed. Mulder and Scully investigate when Mulder suspects this man may have paranormal abilities. The man in question may just be the luckiest man on Earth.
- Five years have passed since Scully escaped from Donnie Pfaster, an obsessed death fetishist. When Reverend Orison helps the madman escape from prison he immediately turns to the one that got away...Scully.
- Mulder and Scully investigate the apparent murder of a magician who was decapitated just minutes after he was able to perform the trick of turning his head around 360 degrees. The agents are perplexed when Scully discovers during the autopsy that the deceased died well before he performed his final trick.