Trong bộ phim, đặc vụ FBI Fox Mulder (David Duchovny) do muốn tìm lại người em gái mất tích của mình, đã dấn thân vào điều tra tại "X-files" với niềm tin rằng em gái của anh đã bị bắt cóc bởi người ngoài Trái Đất. Mulder rất tin tưởng vào sự tồn tại của người ngoài Trái Đất trong khi người tham gia điều tra cùng Fox Mulder là đặc vụ Dana Scully (Gillian Anderson). Ban đầu, Scully không tin vào những điều mà Fox Mulder nói, nhưng với những bằng chứng cụ thể cùng với những vụ án thực tế cô và Mulder trải qua, dần dần Scully đã tin vào những hiện tượng kỳ bí.
Tuy nhiên, tới cuối phim thì nhân vật Fox Mulder xuất hiện ít hơn và có thêm sự xuất hiện của một nhân vật chính khác là đặc vụ John Doggett (Robert Patrick). Tới phiên mình, John Doggett lại nghi ngờ tính xác thực của các vụ án trong X-files và lúc này, chính đặc vụ Scully là người đã khiến cho John Doggett dần dần tin vào X-files
Within (1) 7.3
Ngày phát sóng: 2000-11-05
Thời lượng: 45 min
Tổng quan: 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.
Without (2) 7.4
Ngày phát sóng: 2000-11-12
Thời lượng: 44 min
Tổng quan: 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.
Patience 7.0
Ngày phát sóng: 2000-11-19
Thời lượng: 45 min
Tổng quan: 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.
Roadrunners 7.3
Ngày phát sóng: 2000-11-26
Thời lượng: 45 min
Tổng quan: 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.
Invocation 6.8
Ngày phát sóng: 2000-12-03
Thời lượng: 45 min
Tổng quan: 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.
Redrum 7.1
Ngày phát sóng: 2000-12-10
Thời lượng: 45 min
Tổng quan: 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.
Via Negativa 6.6
Ngày phát sóng: 2000-12-17
Thời lượng: 45 min
Tổng quan: 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.
Surekill 6.5
Ngày phát sóng: 2001-01-07
Thời lượng: 45 min
Tổng quan: 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.
Salvage 6.4
Ngày phát sóng: 2001-01-14
Thời lượng: 44 min
Tổng quan: A man whose blood is rapidly changing into metal alloy enacts revenge on those who caused his condition.
Badlaa 6.3
Ngày phát sóng: 2001-01-21
Thời lượng: 45 min
Tổng quan: 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.
The Gift 6.8
Ngày phát sóng: 2001-02-04
Thời lượng: 45 min
Tổng quan: 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.
Medusa 6.9
Ngày phát sóng: 2001-02-11
Thời lượng: 44 min
Tổng quan: Scully and Doggett must race against the clock to investigate and fight off a contagion lurking in the subway tunnels of Boston.
Per Manum 6.7
Ngày phát sóng: 2001-02-18
Thời lượng: 44 min
Tổng quan: 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.
This Is Not Happening (1) 7.2
Ngày phát sóng: 2001-02-25
Thời lượng: 45 min
Tổng quan: 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.
Deadalive (2) 7.2
Ngày phát sóng: 2001-04-01
Thời lượng: 44 min
Tổng quan: 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.
Three Words 7.3
Ngày phát sóng: 2001-04-08
Thời lượng: 44 min
Tổng quan: 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.
Empedocles 6.5
Ngày phát sóng: 2001-04-22
Thời lượng: 45 min
Tổng quan: Special Agent Reyes enlists Mulder's help in investigating a supernatural killer's connection to the unsolved murder of Agent Doggett's son, Luke.
Vienen 6.9
Ngày phát sóng: 2001-04-29
Thời lượng: 45 min
Tổng quan: 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.
Alone 7.1
Ngày phát sóng: 2001-05-06
Thời lượng: 45 min
Tổng quan: 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.
Essence (1) 7.2
Ngày phát sóng: 2001-05-13
Thời lượng: 44 min
Tổng quan: 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.
Existence (2) 7.6
Ngày phát sóng: 2001-05-20
Thời lượng: 44 min
Tổng quan: 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.
