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- Season 6 overviewNov 8, 1998-May 16, 199922 episodesSeason 6 episodes1. The Beginning Nov 8, 1998
- Partnership of Mulder and Scully is threatened by the hunt for a deadly creature.
- 2. Drive Nov 15, 1998
- Scully tries to determine if the deranged man holding Mulder trapped in a car has a deadly illness.
- 3. Triangle Nov 22, 1998
- Mulder gets into a bizarre conflict on a mysterious ship in the Bermuda Triangle.
- 4. Dreamland Nov 29, 1998
- Mulder and Scully visit Area 51 where they witness the flight of a mysterious craft.
- 5. Dreamland II Dec 6, 1998
- Scully suspects her partner's odd behavior is not what it seems; Mulder needs to reclaim his life.
- 6. How the Ghosts Stole Christmas Dec 13, 1998
- Mulder convinces Scully to help him stake out a haunted house.
- 7. Terms of Endearment Jan 3, 1999
- When a woman is accused of murdering her infant, Mulder and Scully suspect sinister forces.
- 8. The Rain King Jan 10, 1999
- Mulder and Scully meet a man who claims to control the weather.
- 9. S.R. 819 Jan 17, 1999
- When Skinner falls seriously ill, Mulder and Scully suspect foul play.
- 10. Tithonus Jan 24, 1999
- Scully teams with a new partner on a probe into a crime photographer.
- 11. Two Fathers Feb 7, 1999
- Cassandra Spender's reappearance threatens to expose the extraterrestrial conspiracy.
- 12. One Son Feb 14, 1999
- Mulder learns the truth about the conspiracy but isn't sure of his next step.
- 13. Agua Mala Feb 21, 1999
- In Florida during hurricane season, agents probe strange disappearances.
- 14. Monday Feb 28, 1999
- A bad day that keeps getting worse ends inexorably in tragedy.
- 15. Arcadia Mar 7, 1999
- Mulder and Scully pose as a married couple to probe bizarre events at a gated community.
- 16. Alpha Mar 28, 1999
- A mysterious dog thought to be the last of a rare Asian breed is responsible for several murders.
- 17. Trevor Apr 11, 1999
- A convict's accomplished escape from prison is deemed impossible, so Scully and Mulder investigate.
- 18. Milagro Apr 18, 1999
- Scully is attracted to Mulder's chief suspect in a mysterious killing.
- 19. The Unnatural Apr 25, 1999
- An old case involving a star ballplayer from the Negro Leagues is revived.
- 20. Three of a Kind May 2, 1999
- The Lone Gunmen trick Scully into going to Las Vegas to help them.
- 21. Field Trip May 9, 1999
- The skeletons of the victims in a double murder are found in a field.
- 22. Biogenesis May 16, 1999
- The discovery of an ancient artifact and an investigation of its meaning ultimately endanger Mulder.