| A1 |
The Military System (Operation Explanation, Ranking) |
| A2 |
Barracks (Character Select) |
| A3 |
Blue Water Fangs -The Island Of Dr. Moreau- (Main Theme From Metal Slug 3, Stage 1) |
| A4 |
Marine Diver (Stage 1 Alternative Route~Deep Sea) |
| A5 |
The Unknown World (Stage 1 Alternative Route~Core Facility, UFO Interior Passage 1) |
| A6 |
Steel Beast 7beats (Boss Theme A) |
| A7 |
Midnight Wandering (Stage 2) |
| A8 |
Devil's Snow Cave (Stage 1 Alternative Route~Cave Of Ice) |
| B1 |
Metamorphasis (Boss Theme B) |
| B2 |
The Shallow Sea (Stage 3) |
| B3 |
Hard Water (Stage 3 Alternative Route~Underground Channel) |
| B4 |
Assault Theme (Stage 3 Alternative Route~Bridge, Stage 5-2) |
| B5 |
Secret Factory (Stage 3 Alternative Route~Armory) |
| B6 |
Desert (Stage 4) |
| C1 |
Pyramid (Stage 1 Alternative Route~Pyramid) |
| C2 |
The Cenotaph (Stage 4 Alternative Route~Ancient Ruins) |
| C3 |
The Japanese Army (Stage 4 Alternative Route~Ex-Military Hideout) |
| C4 |
Into The Sky (Stage 5-1) |
| C5 |
The Kidnapping (Alien Appearance) |
| C6 |
Into The Cosmos (The Void Of Space) |
| C7 |
Kiss In The Dark (Enemy UFO Interior) |
| D1 |
First Contact (UFO Interior Passage 2) |
| D2 |
Bioinformatics (UFO Interior Passage 2) |
| D3 |
Escape (UFO Escape) |
| D4 |
Final Attack (Final Boss) |
| D5 |
End Title (Final Production~Staff Roll) |
| D6 |
Gravestone (Game Over) |
| D7 |
Carry Out (Stage Clear) |
