6x01 The Beginning
Written by Chris Carter
Directed by Kim Manners
Airdate: 8 November 1998
Mulder and Scully's ability to pursue the X-files - and their partnership - is threatened by the hunt for a deadly creature in the Arizona desert, whose capture may or may not prove Mulder's theories about the existence of extraterrestrial life.
6x02 Drive
Written by Vince Gilligan
Directed by Rob Bowman
Airdate: 15 November 1998
With Mulder trapped in a car by a seemingly deranged man, Scully races to determine if the man is suffering from a deadly illness - and if Mulder is in danger of becoming the next victim.
6x03 Triangle
Written by Chris Carter
Directed by Chris Carter
Airdate: 22 November 1998
A trip to the Bermuda Triangle lands Mulder in the middle of a bizarre conflict on a mysterious ship, with the fate of the world in his hands.
6x04 Dreamland
Written by Vince Gilligan, Frank Spotnitz and John Shiban
Directed by Kim Manners
Airdate: 29 November 1998
An anonymous tip finally brings Mulder and Scully to the mecca of all UFO lore - area 51. but when the agents witness the flight of a mysterious craft, their lives are profoundly - and perhaps irrevocably - altered.
6x05 Dreamland II
Written by Vince Gilligan, Frank Spotnitz and John Shiban
Directed by Kim Manners
Airdate: 6 December 1998
Scully begins to suspect that her partner's strange behavior is more than it appears to be, while Mulder fights to return his life to normal before it's too late.
6x06 How The Ghosts Stole Christmas
Written by Chris Carter
Directed by Chris Carter
Airdate: 13 December 1998
On the night before Christmas, Mulder convinces Scully to put aside her gift wrapping and stake out a reputed haunted house. but they discover a married couple (guest stars lily Tomlin and Edward Asner) living in the house, keeping a secret the agents never expected.
6x07 Terms of Endearment
Written by David Amann
Directed by Rob Bowman
Airdate: 3 January 1999
When a mother is accused of killing her unborn child, Mulder and Scully begin to suspect a more sinister force is at work.
6x08 Rain King
Written by Jeffrey Bell
Directed by Kim Manners
Airdate: 10 January 1999
In a small town plagued by drought, Mulder and Scully come upon a man who claims to be able to control the weather - at a hefty profit. yet the agents discover a force of nature at work, which is even more powerful than the weather.
6x10 S R 819
Written by John Shiban
Directed by Dan Sackheim
Airdate: 17 January 1999
Mulder and Scully have 24 hours to save Assistant Director Skinner from being killed - but in order to do so, they must determine who wants him dead, and why.
6x09 Tithonus
Written by Vince Gilligan
Directed by Michael Watkins
Airdate: 24 January 1999
Paired with a new partner, agent Scully investigates a crime scene photographer whose subjects may in fact be his victims.
6x11 Two Fathers
Written by Frank Spotnitz and Chris Carter
Directed by Kim Manners
Airdate: 7 February 1999
The agents search for answers when Cassandra Spender mysteriously reappears.
6x12 One Son
Written by Chris Carter and Frank Spotnitz
Directed by Rob Bowman
Airdate: 14 February 1999
Mulder learns the truth about the government/alien conspiracy responsible for his sister's abduction, but now faces a greater dilemma: what to do with this new found knowledge.
6x14 Agua Mala
Written by David Amann
Directed by Rob Bowman
Airdate: 21 February 1999
Stranded in Florida by a hurricane, Mulder and Scully seek safety in an old apartment building - but the agents find themselves in even more danger when they learn something else has come in from the rain with them.
6x15 Monday
Written by John Shiban and Vince Gilligan
Directed by Kim Manners
Airdate: 28 February 1999
A bad day keeps getting worse for Mulder and Scully, ending in tragedy that the agents seem powerless to prevent.
6x13 Arcadia
Written by Daniel Arkin
Directed by Michael Watkins
Airdate: 7 March 1999
Mulder and Scully go undercover, posing as a married couple, to investigate strange happenings in a planned suburban community.
6x16 Alpha
Written by Jeffrey Bell
Directed by Peter Markle
Airdate: 28 March 1999
Two crew members aboard the T'ien Kou, a Chinese freighter bound for Los Angeles, sneak into the cargo hold to investigate a large container. One of the crew members pokes at the container and agitates the animal inside to the point that they think it may have killed itself.
6x17 Trevor
Written by Jim Guttridge and Ken Hawrliw
Directed by Rob Bowman
Airdate: 11 April 1999
When a convict makes an impossible escape from a prison, Mulder and Scully must discover his secret before they can find him.
6x18 Milagro
Story by Frank Spotnitz and John Shiban
Teleplay by Chris Carter
Directed by Kim Manners
Airdate: 18 April 1999
While tracking a killer who leaves no clues, agent Scully finds herself strangely attracted to agent Mulder's chief suspect.
6x20 The Unnatural
Written by David Duchovny
Directed by David Duchovny
Airdate: 25 April 1999
Mulder and Scully dig up an old case involving a star player in the Negro baseball league with an unbelievable batting average - and an incredible secret.
6x19 Three of a Kind
Written by Vince Gilligan and John Shiban
Directed by Bryan Spicer
Airdate: 2 May 1999
The Lone Gunmen attend a defense contractors' convention in Las Vegas to uncover trade secrets. when they catch a glimpse of the woman who disappeared from Byers' life ten years previously, they trick Scully into coming to their aid.
6x21 Field Trip
Story by Frank Spotnitz
Teleplay by Vince Gilligan and John Shiban
Directed by Kim Manners
Airdate: 9 May 1999
A mystery involving two skeletons leads the agents on a journey in which nothing is quite as it seems.
6x22 Biogenesis
Written by Chris Carter and Frank Spotnitz
Directed by Rob Bowman
Airdate: 16 May 1999
An ancient artifact is unearthed, striking at the very heart of the X-files - but the search for its meaning takes a grave toll on agent Mulder.