This article contains episode information and plot summaries from the television show The X-Files.
Season nine ran from 2001-2002.
Main and recurring cast can be found on the main X-Files page.
Nothing Important Happened Today
After a chilling series of water-related murders, Doggett investigates when an old military friend of his had unexplainable links. Despite obvious cover-ups, Skinner and Reyes - who has joined the X-Files - assists. Meanwhile Scully and baby William continue on by themselves with Mulder having left.
- David Duchovny is no longer in the main credits. Gillian Anderson and Robert Patrick are joined in the credits by Annabeth Gish - who was listed as 'Also Starring' in season 8, and Mitch Pileggi - who has been listed as 'Also Starring' since the first season.
Nothing Important Happened Today II
- Guest Starring Lucy Lawless as Sharon McMahon
While worrying about the safety of William and his mysterious abilities, Scully unofficially assists Doggett in uncovering the secrets relating to water contamination that are hidden in a clandestine laboratory on board a naval ship. While he learns that Scully was the one who asked Mulder to leave, Reyes attempts to assess the alliances of her ex-boyfriend, Assistant Director Brad Follmer, whom she suspects left the information that almost got them killed.
Dæmonicus
With Scully reassigned to the Quantico Training Academy, Doggett and Reyes investigate their first X-File together — a series of satanic ritual murders - which sees their different investigative techniques working together.
4-D
A vicious murderer threatens Doggett and Reyes and then vanishes, or does he? Doggett is shot and Follmer discovers that Reyes was the shooter, or was she? The only thing certain is that someone is one step ahead of everyone else.
Lord of the Flies
Scully, Reyes and Doggett investigate when a teenager dies while performing a daredevil feat for a cable access show, but his death is soon revealed to be caused by a disturbing family secret.
Trust No 1
- Guest Starring Terry O'Quinn as Shadow Man
- Allison Smith as Patti
- Kathryn Joosten as Agent Edie Boal
Scully is hopeful about reuniting with Mulder when a complete stranger offers new information about what drove him into hiding. Yet her trust in the stranger may place Mulder in even more danger.
John Doe
With no knowledge of his identity or his past, Doggett is found wandering a dusty Mexican town. While he struggles to piece together his memory, he finds himself embroiled in a smuggling plot, and - across the border - Reyes and Scully attempt to find him.
Hellbound
Agent Reyes takes the lead while investigating an X-file case, surrounding a man found skinned alive. When she discovers that he had visions of a similar thing, she calls on Scully's expertise to help on the investigation, which pays off when they find a link to 1960 - a link which may be deeper than it seems.
Provenance
When rubbings from the spaceship resurface, the FBI hides its investigation from the X-Files. Meanwhile, Scully is forced to take drastic measures when she discovers a threat to William.
Providence
Distrustful of both Skinner and Follmer, Scully circumvents the FBI's investigation into the kidnapping and does her own, assisted by Reyes and the Lone Gunmen. Her fears are heightened when she learns Mulder may be dead, and William is kidnapped by the alien cult.
Audrey Pauley
Awakening in a surreal hospital (which a companion believes to be Death's Waiting Room) after being hit by a car, a comatose Agent Reyes struggles to wake herself up before her organ donor card is acted upon. Her only link with the outside world is a possibly autistic woman named Audrey Pauley. Outside, Doggett and Scully begin to suspect that outside forces are conspiring to end her life.
- Quotes
- Doggett: I was thinking about getting a cat.
- Reyes: (laughs) There are cat people, and there are dog people. You're a dog person, John.
Underneath
Doggett is determined to find an error in the DNA evidence that freed the convicted "Screwdriver Killer" who he nearly caught in the act 13 years earlier. But as the case takes several twists, Doggett finds himself at odds with Reyes and Scully as he attempts to prove his theory.
Improbable
In the race to catch a serial killer, Scully and Reyes find themselves relying on numerology, their powers of deduction, and a mysterious and god-like card-playing stranger. Meanwhile Doggett attempts to liaise with the police on the case, and finds that his time on the X-Files has somewhat changed his opinions.
Scary Monsters
- Guest Starring Jolie Jenkins as Agent Leyla Harrison
Agent Harrison takes Reyes and Doggett on a drive into the mountains, after a woman stabs herself repeatedly and her widowed husband refuses to let anyone see their son. When Harrison's young admirer shows up at Scully's door and convinces her to come with him and save them, they discover that monsters under the bed may be more than just the product of a young boy's vivid imagination.
Jump the Shark
When Morris Fletcher approaches the agents with information related to the supersoldiers, they turn to the Lone Gunmen. But the Gunmen and Jimmy are already knee-deep in a bio-terrorist's plot to release a deadly toxin, and his links to the mysterious Yves.
William
Doggett finds a strange disfigured man in the X-Files office, and - on a whim of Scully's - they test his DNA. But the surprising answers they find become even more surprising when William's life is put on the line.
Release
When one of Scully's students displays an inordinate ability to profile serial killers, his insights reopen the murder case of Doggett's son.
Sunshine Days
Doggett, Reyes, Skinner and Scully stumble on to a bizarre murder case where the main suspect is a man with an unusual obsession for The Brady Bunch. Despite their initial differences - both in investigative style and love of The Brady Bunch - the four of them soon learn that the man's telekinetic ability is the ultimate, undeniable proof of an X-File.
The Truth (I and II)
When Fox Mulder is placed under military arrest, Scully and Skinner immediately travel to Virginia to see him. Mulder has been placed under arrest for breaking into a military bunker - where he accessed information on alien technology - and allegedly killing Knowle Rohrer, Doggett's former army friend-turned-supersoldier.
While Mulder receives mysterious visits from phantoms of his past, Scully and Skinner go to great lengths to get him released, but he is ultimately put on trial - a trial with an outcome seemingly set from the start.
Skinner takes Mulder's defense, while Scully, Reyes, Doggett, Marita Covarrubias, Gibson Praise and Jeffrey Spender take the stand. Although they ultimately prove his case - when Scully discovers that the body is not that of Knowle Rohrer - their testimony is overruled and Mulder is sentenced to death.
With the surprising help of Deputy Director Kersh, the group break him free and Mulder and Scully drive off. Despite being told to get out of the country, Mulder drives instead south to New Mexico. Skinner finds himself being called in for a meeting with Toothpick Man and we see him for the last time as the door closes behind him.
In New Mexico, Scully and Mulder arrive at a pueblo where a dying Cigarette-Smoking Man is hiding out to survive the colonisation - an event that will happen on December 22 2012. Outside, Reyes and Doggett face off against Knowle Rohrer, who is ultimately destroyed by the minerals of the pueblo. Switching cars with Mulder and Scully, the agents drive off. The helicopters destroy the pueblo - and the Smoking Man - before giving chase to the wrong car and we last see Doggett and Reyes driving off with them in pursuit.
In a hotel room in New Mexico, Mulder and Scully prepare for bed and talk. Their final words:
SCULLY: You've always said that you want to believe. But believe in what Mulder? If this is the truth that you've been looking for then what is left to believe in?
MULDER: I want to believe that the dead are not lost to us. That they speak to us as part of something greater than us-- greater than any alien force. And if you and I are powerless now, I want to believe that if we listen to what's speaking, it can give us the power to save ourselves.
SCULLY: Then we believe the same thing.
MULDER: Maybe there's hope.
- The last scene mirrors a scene in the pilot where Mulder first opens up to Scully.
