| 1 | Title |
| 2 | Menu Select |
| 3 | Prologue |
| 4 | Frigate Orpheon |
| 5 | VS. Parasite Queen |
| 6 | Frigate Orpheon Escape |
| 7 | Planet Tallon IV |
| 8 | Ancient Chozo Ruins |
| 9 | VS. Hive Totem |
| 10 | VS. Giant Beetle |
| 11 | Chozo Ruins |
| 12 | Energy Core |
| 13 | VS. Flaahgra |
| 14 | Lava Caves (Burning Trail) |
| 15 | Lava Caves |
| 16 | Ice Valley |
| 17 | Ice Chapel |
| 18 | Space Pirates (Laboratory Gate) |
| 19 | VS. Space Pirates |
| 20 | VS. Thardus |
| 21 | Tallon Overworld |
| 22 | Chozo Elder Cathedral |
| 23 | VS. Chozo Ghost |
| 24 | Ice Valley (Phendrana Deep Lake Area) |
| 25 | Crashed Ship Frigate Orpheon |
| 26 | Phazon Mines |
| 27 | Phazon Area |
| 28 | VS. Omega Pirate |
| 29 | Artifact Temple |
| 30 | VS. Meta Ridley |
| 31 | Artifact Temple ~ (Chozo Seal Release) |
| 32 | Impact Crater |
| 33 | VS. Metroid Prime (Spider) |
| 34 | VS. Metroid Prime (Head) |
| 35 | Temple Collapse ~ Epilogue |
| 36 | Ending Staff Roll |
| 37 | End Jingle |
| 38 | Record of Samus |
| 39 | Samus Appearance Jingle |
| 40 | Item Obtainment Jingle |
| 41 | Artifact Obtainment Jingle |
