| Season One | 13 color episodes in 60 minute format | |||
|---|---|---|---|---|
| Ep | PN | Airdate | Title | |
| 1 | 1AEB79 | Mar 04/01 | Pilot | |
| 2 | 1AEB01 | Mar 11/01 | Bond, Jimmy Bond | |
| 3 | 1AEB02 | Mar 16/01 | Eine, Kleine, Frohike | |
| 4 | 1AEB03 | Mar 18/01 | Like Water For Octane | |
| 5 | 1AEB04 | Mar 23/01 | Three Men and a Smoking Diaper | |
| 6 | 1AEB05 | Apr 06/01 | Planet of the Frohikes | |
| 7 | 1AEB06 | Mar 30/01 | Madam, I'm Adam | |
| 8 | 1AEB07 | Apr 13/01 | Maximum Byers | |
| 9 | 1AEB08 | Apr 20/01 | Diagnosis: Jimmy | |
| 10 | 1AEB09 | May 04/01 | The Lying Game | |
| 11 | 1AEB10 | Apr 27/01 | Tango de los Pistoleros | |
| 12 | 1AEB11 | Jun 01/01 | Cap'n Toby | |
| 13 | 1AEB12 | May 11/01 | All About Yves (Part 1) | |
| 9ABX15 | Apr 21/02 | Jump the Shark (Part 2) (The X-Files episode) | ||
| The X-Files crossover episodes | 39 color episodes in 60 minute format | ||
|---|---|---|---|
| Ep | PN | Airdate | Title |
| 17 | 1X16 | Feb 18/94 | E.B.E. |
| 27 | 2X03 | Sep 30/94 | Blood |
| 32 | 2X08 | Nov 11/94 | One Breath |
| 42 | 2X18 | Feb 24/95 | Fearful Symmetry |
| 49 | 2X25 | May 19/95 | Anasazi (Part 1) |
| 50 | 3X01 | Sep 22/95 | The Blessing Way (Part 2) |
| 51 | 3X02 | Sep 29/95 | Paper Clip (Part 3) |
| 58 | 3X09 | Nov 24/95 | Nisei (Part 1) |
| 65 | 3X16 | Feb 16/96 | Apocrypha (Part 2) |
| 72 | 3X23 | May 10/96 | Wetwired |
| 80 | 4X07 | Nov 17/96 | Musings of a Cigarette Smoking Man |
| 87 | 4X14 | Feb 09/97 | Memento Mori |
| 98 | 5X02 | Nov 02/76 | Redux (Part 2) |
| 99 | 5X03 | Nov 09/97 | Redux 2 (Part 3) |
| 100 | 5X01 | Nov 16/97 | Unusual Suspects |
| 104 | 5X07 | Dec 14/97 | Emily (Part 2) |
| 108 | 5X11 | Feb 15/98 | Kill Switch |
| 117 | 5X20 | May 17/98 | The End |
| 120 | 6ABX03 | Nov 22/98 | Triangle |
| 122 | 6ABX05 | Dec 06/98 | Dreamland II |
| 129 | 6ABX12 | Feb 14/99 | One Son (Part 2) |
| 137 | 6ABX19 | May 02/99 | Three of a Kind |
| 138 | 6ABX21 | May 09/99 | Field Trip |
| 152 | 7ABX13 | Feb 27/00 | First Person Shooter |
| 154 | 7ABX15 | Mar 19/00 | En Ami |
| 161 | 7ABX22 | May 21/00 | Requiem (Part 1) |
| 162 | 8ABX01 | Nov 05/00 | Within (Part 2) |
| 168 | 8ABX07 | Dec 17/00 | Via Negativa |
| 172 | 8ABX11 | Feb 04/01 | The Gift |
| 176 | 8ABX15 | Apr 01/01 | Dead Alive (Part 2) |
| 177 | 8ABX18 | Apr 08/01 | Three Words (Part 3) |
| 182 | 8ABX21 | May 19/01 | Existence (Part 2) |
| 183 | 9ABX01 | Nov 11/01 | Nothing Important Happened Today (Part 1) |
| 184 | 9ABX02 | Nov 18/01 | Nothing Important Happened Today 2 (Part 2) |
| 191 | 9ABX10 | Mar 03/02 | Provenance (Part 1) |
| 192 | 9ABX11 | Mar 10/02 | Providence (Part 2) |
| 197 | 9ABX15 | Apr 21/02 | Jump the Shark (The Lone Gunmen series finale) |
| 201/202 | 9ABX19/9ABX20 | May 19/02 | The Truth (120 mins) |
