| # | Title | Artist | Time |
| 1. | in the beginning, there was.... | Deb Lyons | 2:00 |
| 2. | first meeting | Deb Lyons | 2:48 |
| 3. | Xenosaga Ⅱ opening theme | Yuki Kajiura | 2:32 |
| 4. | assault | Deb Lyons | 3:38 |
| 5. | strain~Jin | Deb Lyons | 3:51 |
| 6. | here he comes | Yuki Kajiura | 1:56 |
| 7. | fatal fight (Jin & Margulis) | Deb Lyons, Tokyo Philharmonic Chorus | 4:10 |
| 8. | R&D report | Yuki Kajiura | 1:48 |
| 9. | chase | Yuki Kajiura | 2:36 |
| 10. | surrounded | Yuki Kajiura | 2:51 |
| 11. | lamentation | Yuki Kajiura | 5:20 |
| 12. | Albedo | Yuki Kajiura | 1:56 |
| 13. | communication breakdown | Tokyo Philharmonic Chorus | 4:10 |
| 14. | Sakura (theme-piano ver.) | Yuki Kajiura | 1:35 |
| 15. | Sakura #2 (theme-simple voc.ver.) | Margaret Dorn | 2:28 |
| 16. | strained | Yuki Kajiura | 1:06 |
| 17. | Jr. #2 | Yuriko Kaida | 1:38 |
| 18. | strained #2~Albedo #2 | Yuki Kajiura | 3:51 |
| 19. | in the beginning, there was....#2 | Deb Lyons | 1:56 |
| 20. | battle of Elsa | Yuki Kajiura | 3:02 |
| 21. | here she comes (KOS-MOS) | Yuki Kajiura | 2:35 |
| 22. | battle of Elsa #2 | Yuki Kajiura | 2:06 |
| 23. | gate out | Yuki Kajiura | 3:28 |