| Stage | Agent | Special Agent | Perfect Agent |
| dataDyne Central - Defection | 0:42 | 1:08 | 6:42 |
| dataDyne Research - Investigation | 2:07 | 4:19 | 6:11 |
| dataDyne Central - Extraction | 1:59 | 4:06 | 5:27 |
| Carrington Villa - Hostage One | 1:46 | 2:30 | 11:02 |
| Chicago - Stealth | 0:21 | 1:18 | 1:44 |
| G5 Building - Reconnaissance | 1:34 | 3:27 | 5:41 |
| Area 51 - Infiltration | 2:01 | 4:01 | 7:06 |
| Area 51 - Rescue | 2:39 | 5:46 | 7:06 |
| Area 51 - Escape | 3:28 | 5:55 | 8:22 |
| Air Base - Espionage | 2:13 | 3:08 | 11:41 |
| Air Force One - Antiterrorism | 1:24 | 2:19 | 3:13 |
| Crash Site - Confrontation | 2:42 | 4:11 | 6:22 |
| Pelagic II - Exploration | 1:57 | 6:31 | 7:59 |
| Deep Sea - Nullify Threat | 5:25 | 10:58 | 7:17 |
| Carrington Institute - Defense | 1:41 | 3:05 | 4:36 |
| Attack Ship - Covert Assault | 4:06 | 4:46 | 11:50 |
| Skedar Ruins - Battle Shrine | 3:03 | 4:27 | 5:15 |
| Mr. Blonde's Revenge | 2:06 | 2:10 | 3:31 |
| Maian SOS | 2:44 | 7:49 | 16:11 |
| WAR! | 0:40 | 1:22 | 2:44 |
| The Duel | 0:03 | 0:09 | 0:12 |
| Total Time | 44:41 | 1:23:25 | 2:20:16 |
