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The X-Files
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.
While investigating the discovery of a preserved alien body found in the mountains of Canada, Mulder is contacted by Michael Kritschgau who tells him about a government conspiracy not to keep alien activity a secret, but to make people believe in them without question and Mulder has been the prime target. With the idea that everything he believes is a lie, Mulder appears to take his own life.
Mulder undergoes an experimental form of hypnotherapy to recover his memories about his sister's abduction but the treatment has side effects including psychotic behaviour and Mulder wakes up one morning in a motel room with someone else's blood all over him.
After a man sees a woman trapped inside a bowling alley pin setter, he goes for help and finds police standing next to the 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 retarded man who works at the bowling alley.
Skinner destroys evidence to cover up a woman's death and poses as Agent Mulder to complete the task. Mulder finds out about Skinner's deception and confronts him and Skinner reveals that he is working for the Cigarette Smoking Man in order to obtain a possible cure for Scully's cancer.
Five babies in the same town are all born with tails and the local OB-GYN is blamed for tampering with fertilised eggs. However, Mulder discovers the culprit to be a simple man with a genetic deformity who may have the ability to alter his appearance.
A strange old man foresees events surrounding the use of an experimental flash-freezing compound. Mulder believes that one of the scientists involved has come from the future to stop his own scientific breakthrough from becoming reality.
The investigating into a plane crash lands an FBI agent dead and its main witness in military jail. Looking further into abductee Max Fenig's prior whereabouts, Scully and Mulder find evidence of alien technology, which is intercepted before being brought to light.
A strange woman informs Mulder that NICAP member Max Fenig (see Fallen Angel) has recently died in a plane crash. After observing Max's body, Mulder suggestion that the plane was intercepted by a UFO is rapidly being covered up by the military.
When a US military general is unexplainably murdered in the back of his limousine, a paramilitary group is suspected and they believe it was a soldier whom they liberated from a Vietnam POW camp and is plotting to kill certain corrupt military figures.
Issac Luria, a Jewish man, is killed by a group of teenagers working for a racist shopowner, but one of them is soon strangled to death and the fingerprints on his neck are of Issac. Despite other factors, Mulder becomes convinced that the man has returned from the dead to exact revenge.
Scully's recent failing health is revealed to be inoperable brain cancer which is common among abductees. She meets with other abductees with the same condition and forms a special bond with a dying woman, while Mulder tries to save her from a doctor who may be connected with the abductions.
While Mulder is forced to take a vacation he leaves Scully with an assignment to keep her busy until he returns. She however, 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.
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.
When a deadly yellow rain falls in a migrant workers camp and kills a young woman, Agents Mulder and Scully come to investigate what happened. After questioning the family the agents learn that they believe a mythical creature is responsible for the death and before long Mulder and Scully are on the trail of a mythical beast known as El Chupacabra. Mulder and Scully have to work out where the beast will go next before it can kill anyone else.
Mulder's dreams help him in finding the body of a little girl which re-opens one of his old cases in the Violent Crimes Unit and leads him to believe the killer he captured had more victims and may have taken his sister many years before.
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.
A rock sample taken from Mars is intercepted at an airport and infects a security officer with the Black Cancer, while Mulder is given a tip about potentially dangerous paramilitary operations but is doubtful when the informant turns out to be Alex Krycek. Reluctantly, Mulder accepts Krycek's help and tracks the rock to Russia where he discovers an elaborate test being performed by Russian scientists.
Frohike pieces together and recites to Mulder and Scully what could be the possible life story of the Cigarette Smoking Man; from a young captain in the US Army recruited to assassinate President Kennedy, to becoming the mysterious man in the shadows at the height of a global conspiracy. What measures will the CSM take to ensure that he remains a mystery forever?
When a series of bizarre murders take place in a hospital's plastic surgery unit, Mulder finds a link to the four witches Sabbaths. This leads Mulder and Scully to question if supernatural forces maybe responsible when they begin to suspect a nurse of practicing witchcraft and causing the deaths of the patients.
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.
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 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 person's body in order to survive.
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.
Mulder finds himself with Jeremiah Smith, who will meet his end on a small farm tended to by clones bearing resemblance to Samantha. Meanwhile, the Syndicate suspects a traitor is in their midst and plan a trap. Mrs Mulder survives, in spite of Mulder's failure.
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.
