| Stage | Agent | Special Agent | Perfect Agent |
| dataDyne Central - Defection | 00:10 | 00:51 | 02:28 |
| dataDyne Research - Investigation | 01:36 | 02:20 | 03:57 |
| dataDyne Central - Extraction | 01:02 | 01:57 | 02:26 |
| Carrington Villa - Hostage One | 01:25 | 01:50 | 02:09 |
| Chicago - Stealth | 00:18 | 00:32 | 00:36 |
| G5 Building - Reconnaissance | 01:05 | 01:20 | 01:58 |
| Area 51 - Infiltration | 01:26 | 02:26 | 04:19 |
| Area 51 - Rescue | 01:49 | 02:52 | 04:16 |
| Area 51 - Escape | 02:49 | 04:48 | 05:25 |
| Air Base - Espionage | 01:33 | 02:03 | 02:47 |
| Air Force One - Antiterrorism | 01:06 | 01:43 | 02:09 |
| Crash Site - Confrontation | 01:38 | 02:14 | 03:33 |
| Pelagic II - Exploration | 01:32 | 03:28 | 06:27 |
| Deep Sea - Nullify Threat | 03:26 | 04:12 | 06:47 |
| Carrington Institute - Defense | 01:10 | 02:09 | 02:42 |
| Attack Ship - Covert Assault | 03:18 | 04:45 | 15:03 |
| Skedar Ruins - Battle Shrine | 02:00 | 03:14 | 05:18 |
| Mr. Blonde's Revenge | 02:10 | 02:30 | 02:57 |
| Maian SOS | 02:04 | 03:38 | 10:46 |
| WAR! | 00:32 | 01:09 | 02:05 |
| The Duel | 00:03 | 00:07 | 00:12 |
| Total Time | 32:12 | 50:08 | 01:28:20 |