| 曲名 | 作・編曲者 | 補足 | 順位 |
| Disc 1 | |||
| in the beginning, there was... | 梶浦由記 | 歌：Deb Lyons | |
| first meeting | 歌：Deb Lyons | ||
| Xenosaga II opening theme | ゲームソング369位 | ||
| assault | 歌：Deb Lyons | ||
| strain～Jin | 歌：Deb Lyons | ||
| here he comes | |||
| fatal fight (Jin & Margulis) | 歌：Deb Lyons | 第5回415位 ゲームソング331位 第2回ゲームソング246位 | |
| R&D report | |||
| chase | |||
| surrounded | |||
| lamentation | |||
| Albedo | |||
| communication breakdown | |||
| Sakura (theme-piano ver.) | |||
| Sakura #2 (theme-simple voc.ver.) | 歌：Margaret Dorn | ||
| strained | |||
| Jr. #2 | 歌：貝田由里子 | ||
| strained #2～Albedo #2 | |||
| in the beginning, there was... #2 | 歌：Deb Lyons | ||
| battle of Elsal | |||
| here she comes (KOS-MOS) | |||
| battle of Elsa #2 | |||
| gate out | |||
| Disc 2 | |||
| here he comes #2 | 梶浦由記 | 歌：Deb Lyons | |
| creeping fear | |||
| U-DO～Febronia | |||
| final crisis | |||
| presentiment～Jr. #3 | |||
| a field of battle～bitter #2 | 歌：貝田由里子 | ||
| inside～Sakura #3 | 歌：貝田由里子 | ||
| I am free | |||
| Sakura #4 (theme-gentle strings ver.) | |||
| Sweet Song (Xenosaga II ending theme) | 歌：Margaret Dorn | ||
| Jr. | 歌：Margaret Dorn | ||
| Jr. #4 | |||
| fatal fight #2 | 歌：Deb Lyons | ||
| bitter | 歌：貝田由里子 | ||
| Nephilim | |||
| the image theme of Xenosaga II #piano ver. | 歌：Deb Lyons | ||
| the image theme of Xenosaga II | 歌：Deb Lyons | ||
