| Stage | Agent | Special Agent | Perfect Agent |
| dataDyne Central - Defection | 0:06 | 0:44 | 1:40 |
| dataDyne Research - Investigation | 1:32 | 2:17 | 3:20 |
| dataDyne Central - Extraction | 0:57 | 1:50 | 2:00 |
| Carrington Villa - Hostage One | 1:19 | 1:35 | 2:00 |
| Chicago - Stealth | 0:16 | 0:30 | 0:33 |
| G5 Building - Reconnaissance | 0:52 | 1:05 | 1:30 |
| Area 51 - Infiltration | 1:20 | 2:00 | 3:00 |
| Area 51 - Rescue | 1:37 | 2:35 | 3:20 |
| Area 51 - Escape | 2:38 | 3:50 | 3:55 |
| Air Base - Espionage | 1:22 | 1:55 | 2:30 |
| Air Force One - Antiterrorism | 0:57 | 1:28 | 1:40 |
| Crash Site - Confrontation | 1:26 | 1:38 | 2:05 |
| Pelagic II - Exploration | 1:00 | 2:20 | 2:40 |
| Deep Sea - Nullify Threat | 2:40 | 3:30 | 3:40 |
| Carrington Institute - Defense | 0:57 | 1:40 | 2:10 |
| Attack Ship - Covert Assault | 2:25 | 3:00 | 3:50 |
| Skedar Ruins - Battle Shrine | 1:25 | 1:50 | 2:00 |
| Mr. Blonde's Revenge | 1:35 | 1:38 | 1:40 |
| Maian SOS | 1:45 | 2:20 | 2:40 |
| WAR! | 0:27 | 0:52 | 1:05 |
| The Duel | 0:03 | 0:06 | 0:10 |
| Total Time | 26:39 | 38:43 | 47:28 |