| Stage | Agent | Special Agent | Perfect Agent |
| dataDyne Central - Defection | 0:06 | 0:38 | 1:28 |
| datadyne Central - Investigation | 1:29 | 2:12 | 2:38 |
| dataDyne Central - Extraction | 0:51 | 1:31 | 1:37 |
| Carrington Villa - Hostage One | 1:09 | 1:22 | 1:34 |
| Chicago - Stealth | 0:15 | 0:28 | 0:30 |
| G5 Building - Reconnaissance | 0:40 | 0:47 | 0:59 |
| Area 51 - Infiltration | 1:13 | 1:37 | 1:51 |
| Area 51 - Rescue | 1:27 | 2:20 | 2:48 |
| Area 51 - Escape | 2:24 | 3:16 | 3:19 |
| Air Base - Espionage | 1:15 | 1:44 | 2:06 |
| Air Force One - Antiterrorism | 0:55 | 1:21 | 1:29 |
| Crash Site - Confrontation | 1:16 | 1:29 | 1:56 |
| Pelagic II - Exploration | 0:51 | 1:47 | 2:07 |
| Deep Sea - Nullify Threat | 2:30 | 2:59 | 3:10 |
| Carrington Institute - Defense | 0:53 | 1:29 | 1:44 |
| Attack Ship - Covert Assault | 2:10 | 2:37 | 3:20 |
| Skedar Ruins - Battle Shrine | 1:08 | 1:23 | 1:30 |
| Mr. Blonde's Revenge | 1:24 | 1:27 | 1:30 |
| Maian SOS | 1:39 | 1:53 | 2:15 |
| WAR! | 0:26 | 0:48 | 0:56 |
| The Duel | 0:03 | 0:06 | 0:09 |
| Total Time | 24:04 | 33:14 | 38:56 |