| Stage | Agent | Special Agent | Perfect Agent |
| dataDyne Central - Defection | N/A | N/A | N/A |
| dataDyne Research - Investigation | 1:30 | 2:14 | N/A |
| dataDyne Central - Extraction | 0:56 | N/A | N/A |
| Carrington Villa - Hostage One | 1:02 | 1:20 | N/A |
| Chicago - Stealth | 0:16 | 0:22 | 0:23 |
| G5 Building - Reconnaissance | 0:42 | N/A | N/A |
| Area 51 - Infiltration | 1:09 | N/A | N/A |
| Area 51 - Rescue | N/A | N/A | N/A |
| Area 51 - Escape | N/A | N/A | N/A |
| Air Base - Espionage | N/A | N/A | N/A |
| Air Force One - Antiterrorism | N/A | N/A | N/A |
| 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 | N/A | N/A | N/A |
| Attack Ship - Covert Assault | N/A | N/A | N/A |
| Skedar Ruins - Battle Shrine | N/A | N/A | N/A |
| Mr. Blonde's Revenge | 1:46 | 1:45 | 1:47 |
| Maian SOS | N/A | N/A | N/A |
| WAR! | 0:29 | N/A | N/A |
| The Duel | N/A | N/A | N/A |
| Total Time | N/A | N/A | N/A |
