| Stage | Agent | Special Agent | Perfect Agent |
| dataDyne Central - Defection | 0:41 | 0:59 | 3:20 |
| dataDyne Research - Investigation | 1:40 | 3:57 | 4:53 |
| dataDyne Central - Extraction | 1:33 | 3:21 | 4:48 |
| Carrington Villa - Hostage One | 1:35 | 2:12 | 4:12 |
| Chicago - Stealth | 0:20 | 0:59 | 1:51 |
| G5 Building - Reconnaissance | 1:18 | 1:34 | 2:17 |
| Area 51 - Infiltration | 1:40 | 4:14 | 14:06 |
| Area 51 - Rescue | 2:18 | 3:53 | 12:29 |
| Area 51 - Escape | 3:13 | 5:16 | 6:33 |
| Air Base - Espionage | 1:32 | 2:14 | 3:50 |
| Air Force One - Antiterrorism | 1:27 | 2:27 | 3:51 |
| Crash Site - Confrontation | 2:41 | 3:36 | N/A |
| Pelagic II - Exploration | 2:11 | 5:44 | 7:56 |
| Deep Sea - Nullify Threat | 5:47 | 11:29 | 14:45 |
| Carrington Institute - Defense | 1:23 | 4:34 | N/A |
| Attack Ship - Covert Assault | 3:39 | 5:12 | N/A |
| Skedar Ruins - Battle Shrine | 3:27 | 13:38 | N/A |
| Mr. Blonde's Revenge | 2:01 | 2:14 | 2:39 |
| Maian SOS | 2:15 | 4:30 | N/A |
| WAR! | N/A | N/A | N/A |
| The Duel | 0:04 | 0:10 | 0:20 |
| Total Time | poor | bad | worse |