| Stage | Agent | Special Agent | Perfect Agent |
| dataDyne Central - Defection | 00:38 | 00:54 | 03:26 |
| dataDyne Research - Investigation | 01:38 | 11:21 | N/A |
| dataDyne Central - Extraction | 01:30 | 05:54 | N/A |
| Carrington Villa - Hostage One | 01:32 | 02:22 | N/A |
| Chicago - Stealth | 00:19 | 01:42 | N/A |
| G5 Building - Reconnaissance | 01:13 | 05:33 | 02:45 |
| Area 51 - Infiltration | 01:26 | N/A | N/A |
| Area 51 - Rescue | 01:54 | N/A | N/A |
| Area 51 - Escape | 03:03 | N/A | N/A |
| Air Base - Espionage | 01:29 | 02:14 | N/A |
| Air Force One - Antiterrorism | 01:07 | N/A | N/A |
| Crash Site - Confrontation | 02:08 | N/A | N/A |
| Pelagic II - Exploration | 02:13 | N/A | N/A |
| Deep Sea - Nullify Threat | 04:01 | N/A | N/A |
| Carrington Institute - Defense | 01:03 | N/A | N/A |
| Attack Ship - Covert Assault | 03:25 | N/A | N/A |
| Skedar Ruins - Battle Shrine | 05:48 | N/A | N/A |
| Mr. Blonde's Revenge | 01:58 | 02:01 | N/A |
| Maian SOS | N/A | N/A | N/A |
| WAR! | N/A | N/A | N/A |
| The Duel | 0:04 | 0:08 | 0:13 |
| Total Time | ??? | ??? | ??? |