第 9 季 共 20 集
播出时间：2001年11月12日
第 1 集 Nothing Important Happened Today (1)
播出时间：2001年11月12日
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.
第 2 集 Nothing Important Happened Today II (2)
播出时间：2001年11月19日
Doggett catches up with Shannon McMahon, the woman who the EPA official picked up. She claims to be a super solider and that the people she has killed were poisoning the water supply, and she wants Doggett to expose the truth.
第 3 集 Dæmonicus
播出时间：2001年12月3日
Doggett and Reyes investigate the murder of a couple in West Virginia that has all the signs of a satanic ritual killing. They link the murder to a doctor who is incarcerated in a mental institute, and Doggett becomes convinced that the doctor is orchestrating the crimes from within the hospital.
第 4 集 4-D
播出时间：2001年12月10日
During a stakeout of murderer Irwin Lukesh, Doggett sees Reyes attacked by Lukesh, but then we see Reyes and Doggett in her apartment, apparently both fine. Elsewhere at the same time, Doggett is shot and Lukesh identifies Reyes as the shooter. While Reyes is asked for her badge and gun by A.D. Follmer, and Doggett lies in hospital near death, the conflicting circumstances of the stakeout and Doggett's shooting do not add up and it becomes clear that Lukesh possesses the power to switch between parallel universes and alter the events in each.
第 5 集 Lord of the Flies
播出时间：2001年12月17日
When a stunt on a local cable reality show goes horribly wrong resulting in a man's death, Doggett and Reyes investigate. But when flies pour out of the victims eye sockets, they find themselves relying on Scully's expertise and ask her to join the investigation.
第 6 集 Trust No 1
播出时间：2002年1月7日
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.
第 7 集 John Doe
播出时间：2002年1月14日
Scully and Reyes join forces to try and find Doggett when he goes missing. Doggett has his own problems, having woken up in jail in Mexico suffering from amnesia. With no knowledge of who he is, Doggett is befriended by a local who soon has him working smuggling illegal immigrants across the border.
第 8 集 Hellbound
播出时间：2002年1月28日
Agent Reyes takes the lead while investigating an X-file case, surrounding a man found skinned alive after having visions of seeing other people appearing skinned alive. Reyes calls on Scully's expertise to help on the investigation, which pays off when Scully finds a link to a case from 1960.
第 9 集 Provenance (1)
播出时间：2002年3月4日
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.
第 10 集 Providence (2)
播出时间：2002年3月11日
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.
第 11 集 Audrey Pauley
播出时间：2002年3月18日
After a car accident, Reyes finds herself in a very gray area, while Doggett desperately denies doctors' diagnoses about his partner, who witnesses a strange disappearance.
第 12 集 Underneath
播出时间：2002年4月1日
Scully, Doggett and Reyes investigate an old case that Doggett worked on as a cop in Brooklyn, dubbed "The Screwdriver Killer". They try to determine whether the man who was convicted and has just been released from prison was actually the man responsible for the murders.
第 13 集 Improbable
播出时间：2002年4月8日
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.
第 14 集 Scary Monsters
播出时间：2002年4月15日
Agent Harrison talks Doggett and Reyes into investigating a boy's claim that monsters killed his mother, who was officially determined to have stabbed herself repeatedly.
第 15 集 Jump the Shark
播出时间：2002年4月22日
The agents ask the Lone Gunmen to help find their friendly foe Yves Adele Harlow after former Area 51 Man-In-Black Morris Fletcher claims she is one of the super-soldiers.
第 16 集 William
播出时间：2002年4月29日
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.
第 17 集 Release
播出时间：2002年5月6日
When an FBI cadet with amazing profiling skills approaches Doggett, Reyes, and Scully with a lead on a suspect in a series of recent murders, he claims the same killer is responsible for the death of Doggett's son. The agents find themselves wondering if his knowledge of the deaths is because of his obsession with the cases he has studied at Quantico, or if he is in some way involved in the murders.
第 18 集 Sunshine Days
播出时间：2002年5月13日
Doggett and Reyes investigate a murder outside the house that the original Brady Bunch series was filmed in. The house is owned by a man named Oliver who is obsessed with the show and has rigged the house into a series of traps and changing appearances to look like the Brady house.
第 19 集 The Truth (1)
播出时间：2002年5月20日
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.
第 20 集 The Truth (2)
播出时间：2002年5月20日
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".
