| Stage | Agent | Special Agent | Perfect Agent |
| dataDyne Central - Defection | 0:20 | 0:46 | 2:37 |
| dataDyne Research - Investigation | 1:32 | 2:20 | 3:32 |
| dataDyne Central - Extraction | 0:54 | 1:37 | 1:49 |
| Carrington Villa - Hostage One | 1:18 | 1:39 | 2:17 |
| Chicago - Stealth | 0:16 | 0:33 | 0:36 |
| G5 Building - Reconnaissance | 0:46 | 0:58 | 1:16 |
| Area 51 - Infiltration | 1:18 | 1:57 | 3:08 |
| Area 51 - Rescue | 1:37 | 2:36 | 3:41 |
| Area 51 - Escape | 2:40 | 3:57 | 3:59 |
| Air Base - Espionage | 1:21 | 1:56 | 2:29 |
| Air Force One - Antiterrorism | 0:57 | 1:25 | 1:34 |
| Crash Site - Confrontation | 1:30 | 1:41 | 2:28 |
| Pelagic II - Exploration | 1:00 | 2:12 | 2:42 |
| Deep Sea - Nullify Threat | 3:19 | 4:48 | 3:52 |
| Carrington Institute - Defense | 0:56 | 1:37 | 2:00 |
| Attack Ship - Covert Assault | 2:27 | 2:56 | 4:13 |
| Skedar Ruins - Battle Shrine | 1:25 | 1:54 | 2:09 |
| Mr. Blonde's Revenge | 1:36 | 1:40 | 1:48 |
| Maian SOS | 1:50 | 2:12 | 2:37 |
| WAR! | 0:28 | 0:53 | 1:05 |
| The Duel | 0:03 | 0:06 | 0:09 |
| Total Time | ? | ? | ? |