| Stage | Agent | Special Agent | Perfect Agent |
| dataDyne Central - Defection | 0:14 | 0:46 | 2:16 |
| dataDyne Research - Investigation | 1:35 | 2:20 | 4:30 |
| dataDyne Central - Extraction | 1:07 | 1:56 | 3:59 |
| Carrington Villa - Hostage One | 1:12 | 1:32 | 3:22 |
| Chicago - Stealth | 0:21 | 0:35 | 0:55 |
| G5 Building - Reconnaissance | 1:02 | 1:28 | 1:53 |
| Area 51 - Infiltration | 1:14 | 1:57 | 5:21 |
| Area 51 - Rescue | 1:38 | 2:49 | 5:43 |
| Area 51 - Escape | 2:14 | 4:37 | 5:09 |
| Air Base - Espionage | 1:30 | 1:56 | 3:21 |
| Air Force One - Antiterrorism | 1:06 | 1:34 | 1:38 |
| Crash Site - Confrontation | 1:31 | 1:28 | 4:08 |
| Pelagic II - Exploration | 0:51 | 1:37 | 1:40 |
| Deep Sea - Nullify Threat | 2:34 | 2:55 | 3:57 |
| Carrington Institute - Defense | 0:48 | 1:21 | 1:33 |
| Attack Ship - Covert Assault | 2:52 | 3:26 | 6:40 |
| Skedar Ruins - Battle Shrine | 1:18 | 1:53 | 2:50 |
| Mr. Blonde's Revenge | 2:16 | 2:23 | 2:24 |
| Maian SOS | 2:31 | 3:03 | 3:28 |
| WAR! | 0:30 | 0:46 | 1:08 |
| The Duel | 0:00 | 0:00 | 0:00 |
| Total Time | 28:24 | 40:22 | 1:05:55 |