| 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) |
