| 1. Main Title (2nd Season) | not rated | 0:51 |
| 2. Dead Man's Thoughts | not rated | 2:00 |
| 3. Fish Food | not rated | 3:14 |
| 4. Two Miles Off Jersey | not rated | 2:45 |
| 5. Honey Wagon | not rated | 2:03 |
| 6. Guillotined | not rated | 3:53 |
| 7. Drive For Blood | not rated | 3:29 |
| 8. The Return | not rated | 1:58 |
| 9. Uniforms | not rated | 3:18 |
| 10. Players | not rated | 3:33 |
| 11. Trust Your Pistol | not rated | 0:57 |
| 12. Reanimation | not rated | 1:32 |
| 13. Guardian Angel | not rated | 1:13 |
| 14. Prayer | not rated | 0:47 |
| 15. Suicide Exam | not rated | 2:36 |
| 16. Snake Hold | not rated | 1:25 |
| 17. Hypothermia | not rated | 2:45 |
| 18. Alta | not rated | 2:38 |
| 19. Scully's Discovery / Mulder's E-Mail Message / Skinner Helps Scully | not rated | 8:21 |
| 20. Showdown / Saving Mulder / Faith To Keep Looking | not rated | 11:18 |
| 21. Flesh On Bone | not rated | 4:33 |
| 22. Pustule Package | not rated | 3:24 |
| 23. Eaten By Light | not rated | 2:46 |
| 24. Spontaneous Combustion | not rated | 4:41 |
| 25. Shadow On The Wall | not rated | 2:24 |
| 26. The Mourn | not rated | 3:20 |
| 27. Mercy Wound | not rated | 4:07 |
| 28. Anasazi | not rated | 8:35 |
| 29. Fire In The Mind | not rated | 2:53 |
| 30. A Call To Autopsy | not rated | 1:23 |
| 31. Meet The New Throat | not rated | 4:04 |
| 32. Top Secret Eyes | not rated | 2:24 |
| 33. Spy Boy | not rated | 1:29 |
| 34. Bloody Jacuzzi | not rated | 2:47 |
| 35. Old Files | not rated | 3:08 |
| 36. Blood In The Loaf | not rated | 4:26 |
| 37. Protector | not rated | 5:24 |
| 38. Just Ashes and Bones | not rated | 0:25 |
| 39. Pachyderm | not rated | 2:34 |
| 40. Cat Food | not rated | 3:43 |
| 41. Tiger Walk | not rated | 3:27 |
| 42. Crushed | not rated | 2:44 |
| 43. The X-Files End Credit (Extended #1) | not rated | 0:35 |
| 2:15:52 |
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