| Stage | Agent | Special Agent | Perfect Agent |
| dataDyne Central - Defection | 0:34 | 0:46 | 2:15 |
| dataDyne Research - Investigation | 1:35 | 2:25 | 4:44 |
| dataDyne Central - Extraction | 1:15 | 2:28 | 2:25 |
| Carrington Villa - Hostage One | 1:21 | 2:11 | 3:39 |
| Chicago - Stealth | 0:18 | 0:38 | 0:44 |
| G5 Building - Reconnaissance | 0:56 | 1:11 | 2:06 |
| Area 51 - Infiltration | 1:21 | 2:22 | 4:22 |
| Area 51 - Rescue | 1:47 | 3:37 | 4:38 |
| Area 51 - Escape | 2:40 | 5:39 | 7:38 |
| Air Base - Espionage | 1:25 | 2:34 | 9:32 |
| Air Force One - Antiterrorism | 0:59 | 1:33 | 2:18 |
| Crash Site - Confrontation | 1:34 | 2:50 | 9:13 |
| Pelagic II - Exploration | 1:06 | 3:38 | 4:26 |
| Deep Sea - Nullify Threat | 3:36 | 6:34 | 7:23 |
| Carrington Institute - Defense | 0:57 | 2:12 | 5:37 |
| Attack Ship - Covert Assault | 2:34 | 4:12 | 6:06 |
| Skedar Ruins - Battle Shrine | 1:49 | 3:43 | 5:13 |
| Mr. Blonde's Revenge | 1:36 | 1:47 | 1:46 |
| Maian SOS | 1:52 | 3:13 | 4:16 |
| WAR! | 0:29 | 1:02 | 3:07 |
| The Duel | 0:03 | 0:07 | 0:10 |
| Total Time | 32:17 | 55:13 | 1:35:31 |