| Stage | Agent | Special Agent | Perfect Agent |
| dataDyne Central - Defection | 0:06 | 0:34 | 1:23 |
| dataDyne Research - Investigation | 1:28 | 2:10 | 2:37 |
| dataDyne Central - Extraction | 0:49 | 1:27 | 1:35 |
| Carrington Villa - Hostage One | 1:08 | 1:22 | 1:35 |
| Chicago - Stealth | 0:15 | 0:27 | 0:27 |
| G5 Building - Reconnaissance | 0:38 | 0:43 | 0:53 |
| Area 51 - Infiltration | 1:11 | 1:33 | 1:42 |
| Area 51 - Rescue | 1:25 | 2:18 | 2:44 |
| Area 51 - Escape | 2:23 | 3:17 | 3:22 |
| Air Base - Espionage | 1:15 | 1:43 | 2:05 |
| Air Force One - Antiterrorism | 0:54 | 1:20 | 1:27 |
| Crash Site - Confrontation | 1:15 | 1:27 | 1:52 |
| Pelagic II - Exploration | 0:49 | 1:45 | 2:03 |
| Deep Sea - Nullify Threat | 2:29 | 3:01 | 3:16 |
| Carrington Institute - Defense | 0:52 | 1:28 | 1:39 |
| Attack Ship - Covert Assault | 2:10 | 2:37 | 3:16 |
| Skedar Ruins - Battle Shrine | 1:09 | 1:24 | 1:32 |
| Mr. Blonde's Revenge | 1:22 | 1:24 | 1:28 |
| Maian SOS | 1:37 | 1:53 | 2:07 |
| WAR! | 0:26 | 0:46 | 0:55 |
| The Duel | 0:03 | 0:06 | 0:09 |
| Total Time | ? | ? | ? |