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- Season 9 overviewNov 11, 2001-May 19, 200220 episodesSeason 9 episodes1. Nothing Important Happened Today Nov 11, 2001
- The agents' quest for the truth leads to a conspiracy involving Scully's baby.
- 2. Nothing Important Happened Today II Nov 18, 2001
- Doggett's ongoing search for clues puts his life in jeopardy.
- 3. Daemonicus Dec 2, 2001
- Doggett and Reyes investigate a double murder that has ritualistic elements.
- 4. 4-D Dec 9, 2001
- Agent Reyes is accused of attempting to murder Agent Doggett.
- 5. Lord of the Flies Dec 16, 2001
- A teenager dies while performing a stunt for a television show.
- 6. Trust No. 1 Jan 6, 2002
- Scully lets down her guard when a stranger says he has information about Mulder.
- 7. John Doe Jan 13, 2002
- Doggett wanders a Mexican town with no memory of his identity or his past.
- 8. Hellbound Jan 27, 2002
- Reyes and Doggett investigate a string of murders in which the victims were skinned alive.
- 9. Provenance Mar 3, 2002
- Evidence suggests Scully's baby might be even more "special" than previously imagined.
- 10. Providence Mar 10, 2002
- Scully take matters into her own hands to rescue her son from his kidnappers.
- 11. Audrey Pauley Mar 17, 2002
- Doggett and Scully search for a way to bring Reyes out of a coma before she dies.
- 12. Underneath Mar 31, 2002
- Brutal murders force the reopening of a case Doggett believes he solved years earlier.
- 13. Improbable Apr 7, 2002
- Reyes and Scully receive clues from a mysterious stranger in their hunt for a serial killer.
- 14. Scary Monsters Apr 14, 2002
- The agents investigate a man who may control the monsters that killed his wife.
- 15. Jump the Shark Apr 21, 2002
- The agents enlist the Lone Gunmen to help follow leads regarding the Super Soldiers.
- 16. William Apr 28, 2002
- A severely disfigured man lurking in the office tells Doggett he is seeking information for Mulder.
- 17. Release May 5, 2002
- An FBI trainee connects recent murders to the killing of Doggett's son many years ago.
- 18. Sunshine Days May 12, 2002
- The agents investigate a mysterious death in a suburban neighborhood.
- 19. The Truth May 19, 2002
- On trial for murder, Mulder justifies the existence of the X-Files.
- 20. The Truth II May 19, 2002
- On trial for murder, Mulder justifies the existence of the X-Files.