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The X-Files
After the events of the season six finale, Walter Skinner and Michael Kritschgau are desperately attempting to find the truth behind the so-called alien object. Meanwhile, Fox Mulder is still imprisoned by his own frenetic brain activity. Dana Scully and Skinner are unaware of FBI Special Agent Diana Fowley's duplicity—she is working for The Smoking Man. Scully then travels to Africa to unravel the secrets of the alien artifacts, finding something that looks like a spaceship buried under the shoreline off the Côte d'Ivoire coast. The object may prove that life originated elsewhere, and all religion is based on the Navajo contact with alien life. Unsuccessful, Scully returns from Africa to revisit Mulder in Washington, D.C., but instead she finds out that he has disappeared. She contacts Kritschgau and Skinner to find her partner. The Smoking Man has taken Mulder to a place where all his problems seem to have disappeared. Fowley helps Scully locate Mulder, which leads to her death at the hands of The Smoking Man.
While investigating a bizarre disappearance of a young girl from her home, Mulder becomes obsessed with the number of children who have vanished in similar circumstances. Scully fears that he is emotionally involved due to his sister's disappearance. At the same time it is revealed to him that his mother, Teena Mulder, committed suicide. He then tries to prove that his mother did not take her own life, but is ultimately forced to accept that his mother's death was by her own hand. He is led by a man whose son disappeared years earlier to another truth—that his sister may be among the souls taken by "walk-ins", saving the souls of children doomed to live unhappy lives. Together they locate evidence that proves that Samantha was abducted by The Smoking Man, and was forced to live in a now-abandoned US Army base. It is later revealed that Samantha had become a "walk-in" spirit.
Mulder and Scully return to the town of their first X-Files investigation where a UFO has crashed in the forest. CSM arranges for Krycek to be released from prison in order for him to make contact with the aliens and begin rebuilding the 'Project', while Scully's health appears to be taking a turn.
Mulder and Scully discover a jinniah (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.
The Agents cross paths with a pair of doppelgangers whose close proximity with each other leaves a trail of destruction across 17 states. Mulder and Scully must first understand why this is happening before they can stop it. But the Agents soon realise that the only way to stop the destruction is by stopping the girls meeting up, but this becomes difficult when both fall in love with the same man.
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.
When an employee of Morley Tobacco Co. is apparently killed by tobacco beetles, Mulder suspects that the beetles have hatched inside his lungs and found their way there through inhalation of smoke from an experimental cigarette.
A series of coincidences puts Scully in contact with someone from her past, a married man who she once had an affair with during medical school, but is dying. This causes her to question her romantic and professional choices in her life. Meanwhile Mulder investigates crop circles.
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.
After the miraculous recovery of a young boy who had cancer, Mulder and Scully investigate what has happened but Scully is shocked when The Smoking Man tells her that he cured the boy and offers to show Scully the cure for cancer if she travels with him. But hides her trip from Mulder.
Mulder and Scully are called in to investigate a series of murders where the victims are all in some way related to a wealthy, well-educated doctor. As they search for clues the FBI agents discover the apparent motive is revenge. Years ago the doctor was involved in the euthanasia of a young girl on the verge of death. Once again, Mulder must race against time to find who is behind the killings before the doctor and (more importantly) Scully become the next victims.
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.
A Los Angeles police officer who is being filmed for the show COPS is attacked by a strange monster and Mulder and Scully are investigating the case. Scully is wary of having their faces put on national television but Mulder welcomes the publicity.
After arresting the murderer of Amber-Lynn LaPierre and discovering a mass gravesite 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 young girl unexplainably 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.
Mulder and Scully investigate a gruesome and unexplained snake-bite death, which points to a religious group in the Deep South. Before long the agents realise that the snakes are being used to kill the unrighteous.
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 sawn 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 series of prison breaks bring Agents Mulder and Scully face to face with Scully's former kidnapper, Donnie Pfaster, as Scully is forced to question her faith and confront the clash of morality and religion. But Scully soon learns that Donnie is very keen on going after the one victim that managed to escape him, Dana Scully when Reverend Orison breaks him out of prison...
Mulder and Scully are caught in a real-life Rube Goldberg device as they investigate a man cursed with extremely good luck since he survived a plane crash back in 1989. The man, Henry Weems, insists that he is never unlucky but he finds out that he cannot pass on his good luck to others without severe consequences to their part.
A teenage killer eludes Mulder and Scully by moving too fast for the human eye. Slowly Mulder and Scully realise his ability and try to work out how he gained his power, but not before he goes after his own father, who happens to be the town sheriff. It appears that the killer likes to prey on the emotional vulnerabilities of impressionable kids but can Mulder and Scully put a stop to it before it's too late?
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 4 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 fast-food restaurant is linked to the discovery of a submerged car with a body in the trunk, but no brain in the body. Mulder and Scully investigate further and find that a monster is trying to live a normal life but sometimes has to kill people because of the hunger.
Scully frantically searches for a way to help her ailing partner without having anyone to turn to for help, while a catatonic Mulder's dreams lead him away from his mission and the X-Files to a place which he believes is a better life.
While 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.
The season's storyline picks up directly after last season's finale.
The season takes place fourteen years after the ninth season (2001–02) and seven years after the film The X-Files: I Want to Believe (2008),and follows newly re-instated FBI agents Fox Mulder and Dana Scully as they learn more about the existence of extraterrestrials and their relationship with the government.
After what happened during the season finale of season eight, Fox Mulder goes into hiding. Dana Scully is again reassigned to the FBI Academy and Monica Reyes becomes John Doggett's new FBI partner at the X-Files office. Doggett asks Scully for help on a case involving an EPA official, Carl Wormus, who died after his car was forced off a bridge by a woman he picked up. Doggett and Walter Skinner travel to a reclamation plant, to find any links between Wormus' work and death. After doing an illegal autopsy on Wormus, Alvin Kersh sends Brad Follmer to locate Doggett. The investigation at the reclamation plant leads to an unknown woman, whose identity is later found to be Shannon McMahon, one of Doggett's former Marine associates. She reveals to Doggett that she is a "Super Soldier". This leads them to a clandestine laboratory where a secret experiment is taking place on board on a naval ship. They later find connections with the experiments on the ship to Scully's child, William.
Hopeful about reuniting with Mulder, a complete stranger offers his service to drive Mulder out of hiding. Scully takes the offer, but unknowingly gets herself and Mulder in even more danger. The "Shadow Man", a government agent, follows Scully. It is then discovered that he is a "Super Soldier" bent on killing Scully and Mulder. As confirmed in this episode, a "Super Soldier"'s only weakness is magnetite, which leads to the death of the "Shadow Man". Later on, Scully, Doggett and Reyes find evidence of a dangerous UFO cult which has found a second spacecraft similar to one Scully studied in Africa two years ago. Misled by the FBI, the agents enlist the help of The Lone Gunmen to protect Scully's son after they learn that the UFO cult apparently intend to kill the child. Doggett is run over by a car, leading him to be sent to the local hospital. As Follmer and the "Toothpick Man" are trying to uncover the plans of the three agents, Scully and Reyes leaves Washington, D.C. to find Scully's son.
Scully meets Special Agent John Doggett, the leader of an FBI task force organized to conduct a search for Mulder. Although the search ultimately proves unsuccessful, Doggett is assigned to the X-files and works with Scully to look for explanations to several cases. When Scully learns that several women have reportedly been abducted and impregnated with alien babies, she begins to question her own pregnancy and fears for her unborn child.
After the events of the season six finale, Walter Skinner and Michael Kritschgau are desperately attempting to find the truth behind the so-called alien object. Meanwhile, Fox Mulder is still imprisoned by his own frenetic brain activity. Dana Scully and Skinner are unaware of FBI Special Agent Diana Fowley's duplicity—she is working for The Smoking Man. Scully then travels to Africa to unravel the secrets of the alien artifacts, finding something that looks like a spaceship buried under the shoreline off the Côte d'Ivoire coast. The object may prove that life originated elsewhere, and all religion is based on the Navajo contact with alien life. Unsuccessful, Scully returns from Africa to revisit Mulder in Washington, D.C., but instead she finds out that he has disappeared. She contacts Kritschgau and Skinner to find her partner. The Smoking Man has taken Mulder to a place where all his problems seem to have disappeared. Fowley helps Scully locate Mulder, which leads to her death at the hands of The Smoking Man.
While investigating a bizarre disappearance of a young girl from her home, Mulder becomes obsessed with the number of children who have vanished in similar circumstances. Scully fears that he is emotionally involved due to his sister's disappearance. At the same time it is revealed to him that his mother, Teena Mulder, committed suicide. He then tries to prove that his mother did not take her own life, but is ultimately forced to accept that his mother's death was by her own hand. He is led by a man whose son disappeared years earlier to another truth—that his sister may be among the souls taken by "walk-ins", saving the souls of children doomed to live unhappy lives. Together they locate evidence that proves that Samantha was abducted by The Smoking Man, and was forced to live in a now-abandoned US Army base. It is later revealed that Samantha had become a "walk-in" spirit.
Mulder suspects demon fetal harvesting when a woman claims her unborn child had a horn and tail and was taken by a devil while she slept. While others conclude that the woman killed her own baby, Mulder suspects that her husband is involved and that he may be the devil in disguise.vMulder suspects demon fetal harvesting when a woman claims her unborn child had a horn and tail and was taken by a devil while she slept. While others conclude that the woman killed her own baby, Mulder suspects that her husband is involved and that he may be the devil in disguise.
Scully is suffering from cancer while Mulder is doubtful that aliens exist. The agents fake Mulder's death in an effort to discover which members of the FBI they can trust before individually searching for an answer to Scully's cancer. Her condition worsens, however, and she is hospitalized before Mulder is offered an alleged cure by the Cigarette-Smoking Man. The man also brings Mulder a woman who claims to be his sister, Samantha, although she leaves with the Cigarette-Smoking Man shortly thereafter. When the man offers Mulder a deal to join him, Mulder immediately refuses. He returns to the FBI Headquarters, where he announces that Section Chief Scott Blevins is responsible for Scully's cancer. Both the Section Chief and the Cigarette-Smoking Man are shot. Scully begins to recover and eventually resumes her work on the X-files with Mulder. While staying with her family at Christmas time, she learns that the adopted daughter of a deceased woman is apparently her own child.
When the Syndicate suspect that one of their members is passing information to Mulder and Scully, they organize a canary trap to find the leak, using information about the safety of Mulder's mother as bait. X's role as an informant is discovered, and he is shot dead, although he is able to pass along the name of another informant who can be of use to Mulder—Marita Covarrubias, the Special Representative to the Secretary-General of the United Nations. Covarrubias' aid is sought when Mulder attempts to reach Tunguska in Russia to investigate the source of a further black oil contamination. Whilst there, Mulder is held in a gulag and used as a successful test subject for a black oil vaccine. He escapes and is able to return to America, having found that Alex Krycek is working with the Russians.
Having been diagnosed with cancer, Scully is unsure of her future with the FBI. Mulder is convinced that her condition is a result of her earlier abduction, and is prepared to make a deal with the Syndicate to find a cure. He is dissuaded by Walter Skinner, who secretly makes such a deal instead. While being pursued by an assassin responsible for a hoax alien corpse discovered on a mountaintop, Mulder fakes his own suicide, mutilating the assassin's face to provide a decoy body. He uses the distraction this offers to infiltrate The Pentagon to find a cure for Scully's cancer, while Scully is able to uncover and reveal a Syndicate connection within the FBI.
Investigating evidence of an alien autopsy, Mulder infiltrates a secretive government train carriage carrying an alien-human hybrid. Mulder is almost killed by a Syndicate operative guarding the hybrid, but is saved by his informant X. X had been tipped off about Mulder's activities by the agent's partner Dana Scully. Scully, meanwhile, meets a group of women with abduction experiences similar to her own, and meets another member of the Syndicate known as the First Elder, who claims during her abduction she was placed on a similar train car and experimented upon by the Japanese scientists. The crew of a French salvage ship trying to raise a World War II-era submarine from the sea floor are stricken with massive radiation burns—except for one, who has been infected with a parasitic black oil discovered on the submarine. The oil is controlling the crewman's body, and after passing through several hosts, has overtaken Alex Krycek, who Mulder has been pursuing. Scully finds that the submarine had been involved in discovering the oil on the sea floor during World War II, under the guise of finding a sunken fighter plane. The infected Krycek makes his way to a missile silo used to hide a UFO, and the oil escapes his body to board the craft. Meanwhile, Scully has tracked down Luis Cardinal, the man responsible for killing her sister.
The X-Files are no more. Shut down by the FBI, Scully and Mulder have been reassigned. New supernatural events prove that the X-Files investigations are a necessity and Walter Skinner restores them but with a new team, Fox Mulder and Alex Krycek. Mental patient and alien abductee Duane Barry kidnaps Scully and takes her to a mountain where she disappears. Krycek murders Barry. He works for the Cigarette Smoking Man and disappears with his true loyalties revealed. Scully is returned on the edge of death and Mulder faces a critical choice, seek to ambush members of the conspiracy with the help of his new source Mr. X or stay by Scully's bedside. He chooses Scully. Scully recovers and rejoins Mulder on the X-Files.
FBI Special Agent Dana Scully is assigned to work with Fox Mulder on a group of unexplained cases labeled as X-files. Mulder believes that the paranormal can explain most of the cases, whereas Scully is more interested in finding a scientific, logical explanation. Her first case with Mulder involved a series of unexplainable deaths of young people in a small Oregon town. Mulder fears that Scully may be a spy for the higher ups at the FBI but still boldly theorizes that it is the work of extraterrestrials. Discovering a non-Human corpse in the coffin of one of the victims they exhume doesn't dissuade Scully's skepticism but as the strange occurrences such as time loss, flashes of light, and strange implants in the corpse mount up even she is willing to believe Mulder's theory a bit. When she comes to Mulder fearing she has the same marks as the victims on her own back, he tells her they are merely mosquito bites. Seeing her vulnerable and embarrassed, he asks her to stay and they get to talking. He confides about the disappearance of his sister Samantha Mulder, his FBI career and study of the supernatural & the X-Files, and of a conspiracy to suppress his work on the X-Files. Scully may not believe everything he is saying but a bond has formed between them.
