| Stage | Agent | Special Agent | Perfect Agent |
| dataDyne Central - Defection | 0:07 | N/A | N/A |
| dataDyne Research - Investigation | 1:31 | 2:15 | N/A |
| dataDyne Central - Extraction | 0:50 | 1:33 | 1:48 |
| Carrington Villa - Hostage One | N/A | N/A | N/A |
| Chicago - Stealth | N/A | N/A | N/A |
| G5 Building - Reconnaissance | N/A | N/A | N/A |
| Area 51 - Infiltration | 1:13 | N/A | N/A |
| Area 51 - Rescue | N/A | 2:29 | N/A |
| Area 51 - Escape | N/A | 3:50 | 3:54 |
| Air Base - Espionage | 1:16 | 1:46 | 2:06 |
| Air Force One - Antiterrorism | 0:55 | 1:21 | 1:28 |
| Crash Site - Confrontation | N/A | N/A | N/A |
| Pelagic II - Exploration | N/A | N/A | N/A |
| Deep Sea - Nullify Threat | N/A | N/A | N/A |
| Carrington Institute - Defense | 0:54 | 1:32 | 1:48 |
| Attack Ship - Covert Assault | N/A | N/A | N/A |
| Skedar Ruins - Battle Shrine | N/A | N/A | N/A |
| Mr. Blonde's Revenge | N/A | N/A | N/A |
| Maian SOS | 1:45 | N/A | N/A |
| WAR! | 0:27 | 0:52 | 0:57 |
| The Duel | 0:03 | N/A | N/A |
| Total Time | ?? | ?? | ?? |