| Stage | Agent | Special Agent | Perfect Agent |
| dataDyne Central - Defection | 0:06 | 0:38 | 1:33 |
| dataDyne Research - Investigation | 1:29 | 2:13 | 2:42 |
| dataDyne Central - Extraction | 0:50 | 1:29 | 1:40 |
| Carrington Villa - Hostage One | 1:09 | 1:22 | 1:41 |
| Chicago - Stealth | 0:15 | 0:27 | 0:28 |
| G5 Building - Reconnaissance | 0:40 | 0:47 | 0:58 |
| Area 51 - Infiltration | 1:11 | 1:40 | 1:58 |
| Area 51 - Rescue | 1:28 | 2:22 | 3:05 |
| Area 51 - Escape | 2:28 | 3:28 | 3:34 |
| Air Base - Espionage | 1:15 | 1:46 | 2:15 |
| Air Force One - Antiterrorism | 0:54 | 1:21 | 1:29 |
| Crash Site - Confrontation | 1:19 | 1:32 | 1:58 |
| Pelagic II - Exploration | 0:52 | 1:54 | 2:17 |
| Deep Sea - Nullify Threat | 2:33 | 3:12 | 3:33 |
| Carrington Institute - Defense | 0:52 | 1:29 | 1:48 |
| Attack Ship - Covert Assault | 2:13 | 2:44 | 3:26 |
| Skedar Ruins - Battle Shrine | 1:10 | 1:26 | 1:34 |
| Mr. Blonde's Revenge | 1:24 | 1:29 | 1:30 |
| Maian SOS | 1:41 | 1:58 | 2:13 |
| WAR! | 0:26 | 0:48 | 0:56 |
| The Duel | 0:03 | 0:06 | 0:09 |
| Total Time | 24:18 | 34:11 | 40:47 |