9x01 Nothing Important Happened Today
Written by Chris Carter and Frank Spotnitz
Directed by Kim Manners
Original Airdate: 11 November 2001
While forces inside the establishment attempt to stifle them, the agents find a connection to their case with suspicious murders related to water.
9x02 Nothing Important Happened Today II
Written by Chris Carter and Frank Spotnitz
Directed by Tony Wharmby
Original airdate: 18 November 2001
Scully unofficially assists Doggett and Reyes in uncovering the secrets relating to water contamination that are hidden in a clandestine laboratory on board a naval ship.
9x03 Dæmonicus
Written by Frank Spotnitz
Directed by Frank Spotnitz
Original Airdate: 2 December 2001
With Scully re-assigned to Quantico Training Academy, Doggett and Reyes investigate their first X-File together – a series of satanic ritual murders whose victims may include the agents themselves.
9x05 4-D
Written by Steven Maeda
Directed by Tony Wharmby
Original Airdate: 9 December 2001
A vicious murderer threatens Doggett and Reyes. Or does he? The only certain thing is that he's one step ahead of everyone else.
9x06 Lord of the Flies
Written by Thomas Schnauz
Directed by Kim Manners
Original Airdate: 16 December 2001
A teenager dies while performing a daredevil feat for a cable access show. But his death may be caused by something more sinister than the stunt itself.
9x08 Trust No 1
Written by Chris Carter and Frank Spotnitz
Directed by Tony Whamby
Original Airdate: 6 January 2002
Scully is hopeful of reuniting with Mulder when a complete stranger offers new information about what drove him into hiding. Yet her trust in this stranger may place Mulder in even more danger.
9x07 John Doe
Written by Vince Gilligan
Directed by Michelle MacLaren
Original Airdate: 13 January 2002
With no knowledge of his identity or his past, Doggett is found wandering a dusty Mexican town. He struggles to piece together his memory, how he lost it, and why he is stuck in a foreign place.
9x04 Hellbound
Written by David Amann
Directed by Kim Manners
Original Airdate: 27 January 2002
Convinced it is an X-File, Reyes is drawn to a murder where the victim has been skinned alive. Yet she is unsure why she has such a strange connection to the case.
9x10 Provenance
Written by Chris Carter and Frank Spotnitz
Directed by Kim Manners
Original Airdate: 3 March 2002
When rubbings from the spaceship resurface, the FBI hides its investigation from the X-Files and the one person who is familiar with the symbols' significance – Scully.
9x11 Providence
Written by Chris Carter and Frank Spotnitz
Directed by Chris Carter
Original Airdate: 10 March 2002
After learning that Mulder might be dead, Scully's fears are heightened when William is kidnapped by the alien cult.
9x13 Audrey Pauley
Written by Steven Maeda
Directed by Kim Manners
Original Airdate: 17 March 2002
Doggett and Scully look for answers that will save Reyes' life after she is injured in a horrible car accident. Yet Reyes is also fighting to stay alive in the netherworld between life and death.
9x09 Underneath
Written by John Shiban
Directed by John Shiban
Original Airdate: 31 March 2002
When a case from his past is re-opened, Doggett holds steadfast to his conclusions, which puts him at odds with Scully and Reyes' theories.
9x14 Improbable
Written by Chris Carter
Directed by Chris Carter
Original Airdate: 7 April 2002
The agents rely on numerology, their powers of deduction and a mysterious stranger to help catch a serial killer.
9x12 Scary Monsters
Written by Thomas Schnauz
Directed by Dwight Little
Original Airdate: 14 April 2002
Monster hiding under a little boy's bed may be more than just the product of a vivid imagination.
9x15 Jump The Shark
Written by Vince Gilligan, John Shiban, Frank Spotnitz
Directed by Cliff Bole
Original Airdate: 21 April 2002
When Morris Fletcher approaches the agents with information related to supersoldiers, they turn to the Lone Gunmen. The Gunmen, however, are knee-deep in a bio-terrorist's plot to release a deadly toxin.
Commentary by Frank Spotnitz, Vince Gilligan, and John Shiban
9x17 William
Teleplay by Chris Carter
Story by David Duchovny, Frank Spotnitz, Chris Carter
Directed by David Duchovny
Original Airdate: 28 April 2002
Scully questions whether a disfigured man is really Mulder. But things become even more complicated when the mysterious stranger poses a threat to her son.
9x16 Release
Teleplay by David Amann
Story by John Shiban and David Amann
Directed by Kim Manners
Original Airdate: 5 May 2002
One of Scully's students displays an inordinate ability to profile serial killers. And his insights re-open the murder case of Doggett's son.
9x18 Sunshine Days
Written by Vince Gilligan
Directed by Vince Gilligan
Original Airdate: 12 May 2002
One man's obsession with a 1970s sitcom combined with his remarkable telekinetic ability lead the agents to believe that they have discovered proof for the ultimate X-File.
9x19 and 9x20 The Truth
Written by Chris Carter
Directed by Kim Manners
Original Airdate: 19 May 2002
Mulder's return leads to his being tried before a military tribunal that seeks to justify and prove the very existence of an alien conspiracy – and the X-Files.