| 1. Prologue | not rated | 1:56 |
| 2. Gamera 3: Incomplete Struggle Main Title | not rated | 2:04 |
| 3. The Nightmares | not rated | 0:35 |
| 4. Heaven and Earth Are Evil, Destroy Them | not rated | 1:11 |
| 5. The Discovery | not rated | 1:18 |
| 6. The Seal | not rated | 0:39 |
| 7. Ryuseicho | not rated | 1:29 |
| 8. Catastrophe | not rated | 2:11 |
| 9. The Destruction of Shibuya | not rated | 2:46 |
| 10. Hatred | not rated | 0:34 |
| 11. Birth | not rated | 0:32 |
| 12. Irys | not rated | 1:39 |
| 13. The Shrine Sword | not rated | 0:33 |
| 14. Alien Life Form | not rated | 0:47 |
| 15. Fusion | not rated | 2:09 |
| 16. Manna | not rated | 1:05 |
| 17. The Cocoon | not rated | 1:39 |
| 18. Bizarre Occurrence | not rated | 1:09 |
| 19. The Investigation | not rated | 1:14 |
| 20. The Black, Curved Jewels | not rated | 0:38 |
| 21. Chromosome Samples | not rated | 0:43 |
| 22. Response | not rated | 1:08 |
| 23. The Evil Deity Awakens | not rated | 0:54 |
| 24. The Self-Defense Forces Mobilizes | not rated | 0:41 |
| 25. Imago Irys | not rated | 0:24 |
| 26. The Mystery of Gamera | not rated | 0:53 |
| 27. Mutant | not rated | 0:59 |
| 28. Resolve: Theme Song Variation | not rated | 0:39 |
| 29. Flight | not rated | 0:18 |
| 30. Offense and Defense | not rated | 2:34 |
| 31. Aerial Battle | not rated | 1:00 |
| 32. The Advent of Irys | not rated | 1:12 |
| 33. Descendants From Antiquity | not rated | 1:02 |
| 34. Kyoto Goes Up In Flames | not rated | 1:10 |
| 35. Crash | not rated | 2:45 |
| 36. Ayana and Irys | not rated | 1:26 |
| 37. Gamera...Dead?!? | not rated | 0:32 |
| 38. The Confrontation | not rated | 1:14 |
| 39. Reminiscing | not rated | 1:40 |
| 40. Desperation | not rated | 1:51 |
| 41. Roaring Flame | not rated | 1:15 |
| 42. The Guardian Beast | not rated | 3:18 |
| 43. Ending Theme: Gamera 1999 | not rated | 1:54 |
| 55:40 |
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