| Stage | Agent | Special Agent | Perfect Agent |
| dataDyne Central - Defection | 00:18 | 00:53 | 04:16 |
| dataDyne Research - Investigation | 01:31 | 02:24 | 06:21 |
| dataDyne Central - Extraction | 01:05 | 02:23 | 03:43 |
| Carrington Villa - Hostage One | 01:21 | 01:58 | 04:38 |
| Chicago - Stealth | 00:20 | 00:46 | 01:45 |
| G5 Building - Reconnaissance | 00:53 | 01:09 | 01:38 |
| Area 51 - Infiltration | 01:19 | 03:11 | 06:44 |
| Area 51 - Rescue | 01:45 | 03:15 | 06:15 |
| Area 51 - Escape | 02:42 | 04:56 | 05:17 |
| Air Base - Espionage | 01:26 | 02:27 | 05:09 |
| Air Force One - Antiterrorism | 01:05 | 01:41 | 02:27 |
| Crash Site - Confrontation | 01:51 | 02:56 | 05:29 |
| Pelagic II - Exploration | 01:11 | 02:54 | 07:50 |
| Deep Sea - Nullify Threat | 03:36 | 05:55 | 06:55 |
| Carrington Institute - Defense | 01:00 | 02:05 | 02:39 |
| Attack Ship - Covert Assault | 03:07 | 04:36 | 07:52 |
| Skedar Ruins - Battle Shrine | 02:32 | 04:00 | 04:20 |
| Mr. Blonde's Revenge | 01:49 | 01:57 | 02:19 |
| Maian SOS | 02:05 | 03:01 | 03:53 |
| WAR! | 0:28 | 1:06 | 1:32 |
| The Duel | 00:03 | 00:07 | 00:15 |
| Total Time | ?? | ?? | ?? |