| CD1 |
| 1. The X-Files Main Title (Season One) | not rated | 0:48 |
| 2. Pilot: Scully To DC/Scully Meets Mulder | not rated | 1:20 |
| 3. Pilot: The Close Encounter | not rated | 2:15 |
| 4. Pilot: Scully & FBI Goon | not rated | 0:35 |
| 5. Pilot: FBI Secret Vaults | not rated | 1:14 |
| 6. Squeeze: Hidden Away | not rated | 1:37 |
| 7. Squeeze: Slimed | not rated | 0:41 |
| 8. Squeeze: Cuffed And Tubbed | not rated | 2:15 |
| 9. Fallen Angel: On The Waterfront/Suspended Max | not rated | 6:10 |
| 10. Roland: Sweeper | not rated | 1:46 |
| 11. Roland: Out The Window | not rated | 1:29 |
| 12. Roland: Ramblin' Roland | not rated | 2:05 |
| 13. The Erlenmeyer Flask: Green Goo Chase | not rated | 2:12 |
| 14. The Erlenmeyer Flask: The Wells Brain | not rated | 5:16 |
| 15. Little Green Men: Dead Man's Thoughts | not rated | 2:00 |
| 16. Little Green Men: Fish Food | not rated | 3:14 |
| 17. The Host: Two Miles Off Jersey | not rated | 2:44 |
| 18. The Host: Honey Wagon | not rated | 2:03 |
| 19. The Host: Guillotined | not rated | 3:53 |
| 20. One Breath: The Return | not rated | 1:58 |
| 21. One Breath: Uniforms | not rated | 3:18 |
| 22. One Breath: Players | not rated | 3:33 |
| 23. One Breath: Trust Your Pistol | not rated | 0:57 |
| 24. One Breath: Reanimation | not rated | 1:32 |
| 25. One Breath: Guardian Angel | not rated | 1:13 |
| 26. Anasazi: The Mourn | not rated | 3:20 |
| 27. Anasazi: Mercy Wound | not rated | 4:07 |
| 28. Anasazi: Anasazi | not rated | 8:35 |
| 29. The X-Files End Credits (Extended Remix) | not rated | 0:35 |
| 1:12:59 |
| CD2 |
| 1. The X-Files - Main Title (Short) | not rated | 0:37 |
| 2. Nisei: Choo Choo Sushi | not rated | 4:09 |
| 3. Nisei: Rail Song | not rated | 6:41 |
| 4. 731: Graves | not rated | 2:54 |
| 5. 731: Derailed | not rated | 11:53 |
| 6. Piper Maru: Back in the Hood | not rated | 4:50 |
| 7. Jose Chung's From Outer Space: Harold & Chrissy | not rated | 2:27 |
| 8. Jose Chung's From Outer Space: Closure | not rated | 4:44 |
| 9. The Field Where I Died: Dim Memories | not rated | 1:05 |
| 10. The Field Where I Died: Jonestown Cocktail | not rated | 6:23 |
| 11. Musings of a Cigarette Smoking Man: Extra-Ordinary Men | not rated | 2:09 |
| 12. Musings of a Cigarette Smoking Man: A Place in History | not rated | 6:03 |
| 13. Musings of a Cigarette Smoking Man: Respect | not rated | 1:37 |
| 14. Paper Hearts: El Camino | not rated | 6:38 |
| 15. Paper Hearts: Watergate Heart | not rated | 2:31 |
| 16. Kaddish: Hanging Boy | not rated | 2:47 |
| 17. Kaddish: Spirit Wedding | not rated | 9:14 |
| 18. The X-Files End Credits (Extended Remix) | not rated | 2:11 |
| 1:19:02 |
| CD3 |
| 1. The X-Files Main Title (Remix - Short) | not rated | 0:37 |
| 2. The Post Modern Prometheus: JJ's Diner | not rated | 1:49 |
| 3. The Post Modern Prometheus: Post-Modern Posse | not rated | 9:19 |
| 4. Christmas Carol: Mother Genes | not rated | 3:53 |
| 5. Emily: Little Box of Sand | not rated | 7:36 |
| 6. The End: Closure | not rated | 8:07 |
| 7. Triangle: Quest for Swath | not rated | 8:49 |
| 8. Dreamland: Roadblock | not rated | 1:05 |
| 9. Dreamland: Home Sweet Home | not rated | 2:14 |
| 10. Dreamland: The Imposter | not rated | 6:31 |
| 11. Dreamland II: A Brief History of Fox | not rated | 1:26 |
| 12. Dreamland II: Number 42 | not rated | 1:56 |
| 13. How the Ghosts Stole Christmas: House Organ/Irrational Fear | not rated | 4:39 |
| 14. How the Ghosts Stole Christmas: Bricks | not rated | 0:39 |
| 15. How the Ghosts Stole Christmas: Piano on the Track | not rated | 1:27 |
| 16. How the Ghosts Stole Christmas: Fair Warning | not rated | 3:02 |
| 17. How the Ghosts Stole Christmas: Star Crossed Bullets | not rated | 3:04 |
| 18. How the Ghosts Stole Christmas: A Gift | not rated | 1:44 |
| 19. Two Fathers: The Patriarch | not rated | 2:22 |
| 20. Two Fathers: A Mother's Abduction | not rated | 3:01 |
| 21. One Son: Train Tune | not rated | 4:46 |
| 22. The X-Files End Credit (Extended #2) | not rated | 1:31 |
| 1:19:48 |
| CD4 |
| 1. The X-Files Main Title (7th Season) | not rated | 0:48 |
| 2. The Goldberg Variation: Five Cards | not rated | 3:08 |
| 3. The Sixth Extinction: Sea of Blood | not rated | 5:56 |
| 4. The Sixth Extinction II - Amor Fati: The Martyr | not rated | 1:28 |
| 5. Millennium: The Smell of Zombies | not rated | 5:00 |
| 6. Millennium: The End of the Crusade | not rated | 2:18 |
| 7. All Things: Waterson | not rated | 3:12 |
| 8. Hollywood A.D.: Sniper Zombies | not rated | 3:40 |
| 9. Hollywood A.D.: Dancing Bones | not rated | 2:17 |
| 10. Hollywood A.D.: Hollywood | not rated | 1:04 |
| 11. Hollywood A.D.: The Kiss | not rated | 1:03 |
| 12. Within: Scully's Serenade | not rated | 1:37 |
| 13. Without: Hide & Seek | not rated | 2:03 |
| 14. This Is Not Happening: Starspeak | not rated | 2:57 |
| 15. This Is Not Happening: Hidden Truths/Big Happening | not rated | 3:21 |
| 16. Jump the Shark: Triangle | not rated | 0:40 |
| 17. Jump the Shark: Weird Organs | not rated | 2:01 |
| 18. Jump the Shark: Lone Gunmen Requiem | not rated | 8:12 |
| 19. Release: The Tip | not rated | 2:33 |
| 20. Release: A Synopsis & Release | not rated | 5:38 |
| 21. The Truth Part 1: Mount Weather | not rated | 6:31 |
| 22. The Truth Part 2: Scary Story/For Whom the Smole Blows | not rated | 7:26 |
| 23. The Truth Part 2: The Truth is Inside | not rated | 3:00 |
| 24. The X-Files Main Title (Remix) | not rated | 3:25 |
| 25. I Made This/20th Century Fox Fanfare | not rated | 0:08 |
| 1:19:38 |
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