| Stage | Agent | Special Agent | Perfect Agent |
| dataDyne Central - Defection | 0:06 | 0:35 | 1:25 |
| dataDyne Research - Investigation | 1:28 | 2:09 | 2:38 |
| dataDyne Central - Extraction | 0:49 | 1:22 | 1:35 |
| Carrington Villa - Hostage One | 1:08 | 1:19 | 1:35 |
| Chicago - Stealth | 0:15 | 0:27 | 0:28 |
| G5 Building - Reconnaissance | 0:40 | 0:47 | 0:57 |
| Area 51 - Infiltration | 1:11 | 1:34 | 1:51 |
| Area 51 - Rescue | 1:27 | 2:20 | 2:49 |
| Area 51 - Escape | 2:26 | 3:22 | 3:23 |
| Air Base - Espionage | 1:15 | 1:44 | 2:11 |
| Air Force One - Antiterrorism | 0:54 | 1:21 | 1:28 |
| Crash Site - Confrontation | 1:17 | 1:28 | 1:55 |
| Pelagic II - Exploration | 0:50 | 1:51 | 2:13 |
| Deep Sea - Nullify Threat | 2:40 | 3:11 | 3:14 |
| Carrington Institute - Defense | 0:52 | 1:28 | 1:42 |
| Attack Ship - Covert Assault | 2:10 | 2:38 | 3:20 |
| Skedar Ruins - Battle Shrine | 1:10 | 1:26 | 1:37 |
| Mr. Blonde's Revenge | 1:19 | 1:21 | 1:24 |
| Maian SOS | 1:37 | 1:54 | 2:11 |
| WAR! | 0:26 | 0:46 | 0:54 |
| The Duel | 0:03 | 0:06 | 0:09 |
| Total Time | 24:03 | 33:09 | 38:59 |