| 1 | Title Theme |
| 2 | Menu Select |
| 3 | Prologue |
| 4 | Landing on Aether |
| 5 | Landing Site |
| 6 | Landing Site (Inside Splinter Hive) |
| 7 | Hive Tunnel |
| 8 | VS. Dark Troopers |
| 9 | The Ing |
| 10 | Save Station |
| 11 | Elevator Room |
| 12 | Temple Grounds (Industrial Site) |
| 13 | Gates Of Judgment |
| 14 | Temple Grounds |
| 15 | Last Stand |
| 16 | Doomed Mission |
| 17 | VS. Ing |
| 18 | The Luminoth |
| 19 | Luminoth Energy Controller |
| 20 | Luminoth Item Collect |
| 21 | Light Temple |
| 22 | Agon Wastes |
| 23 | Space Pirates Appear |
| 24 | VS. Space Pirates |
| 25 | Pirate Fear |
| 26 | VS. Guardian Ing |
| 27 | Silence |
| 28 | Dark Samus Appears |
| 29 | VS. Dark Samus |
| 30 | Puzzle Theme |
| 31 | Dark Agon Wastes |
| 32 | VS. Amorbis |
| 33 | Torvus Bog Entrance |
| 34 | Torvus Bog |
| 35 | Dark Torvus Bog |
| 36 | Submerged Temple |
| 37 | Dark Submerged Temple |
| 38 | VS. Chykha Larva |
| 39 | VS. Adult Chykha |
| 40 | Dark Energy Controller |
| 41 | Sanctuary Fortress |
| 42 | Dark Sanctuary Fortress |
| 43 | Dynamo Core |
| 44 | VS. Quadraxis |
| 45 | Sky Temple Gateway |
| 46 | Sky Temple |
| 47 | VS. Emperor Ing (Phase 1) |
| 48 | VS. Emperor Ing (Phase 2) |
| 49 | Final Energy Collected |
| 50 | Escape |
| 51 | Escape from Dark Aether |
| 52 | Dark Aether |
| 53 | Destruction of Dark Aether |
| 54 | Gratitude of the Luminoth |
| 55 | Samus Identity |
| 56 | Mission Accomplished |
| 57 | Hidden Ending |
| 58 | Staff Roll |
| 59 | Record Of Samus |
| 60 | Multiplayer – Hunters |
| 61 | Multiplayer – Hunters (Speed Up) |
| 62 | Multiplayer – Dark Echoes |
| 63 | Samus Aran Appearance Fanfare |
| 64 | Small Item Collection Fanfare |
| 65 | Item Collection Fanfare |
| 66 | Event Jingle |
| 67 | Temple Key Collection Fanfare |
| 68 | Mission Over |
