| Stage | Agent | Special Agent | Perfect Agent |
|---|---|---|---|
| dataDyne Central - Defection | 0:06 | 0:35 | 1:26 |
| dataDyne Research - Investigation | 1:29 | 2:12 | 2:38 |
| dataDyne Central - Extraction | 0:50 | 1:31 | 1:40 |
| Carrington Villa - Hostage One | 1:07 | 1:19 | 1:35 |
| Chicago - Stealth | 0:15 | 0:28 | 0:29 |
| G5 Building - Reconnaissance | 0:40 | 0:47 | 0:58 |
| Area 51 - Infiltration | 1:11 | 1:35 | 1:48 |
| Area 51 - Rescue | 1:28 | 2:20 | 2:48 |
| Area 51 - Escape | 2:26 | 3:22 | 3:22 |
| Air Base - Espionage | 1:15 | 1:44 | 2:09 |
| Air Force One - Antiterrorism | 0:55 | 1:21 | 1:27 |
| Crash Site - Confrontation | 1:18 | 1:29 | 1:53 |
| Pelagic II - Exploration | 0:51 | 1:47 | 2:14 |
| Deep Sea - Nullify Threat | 2:28 | 3:01 | 3:19 |
| Carrington Institute - Defense | 0:52 | 1:29 | 1:44 |
| Attack Ship - Covert Assault | 2:10 | 2:37 | 3:16 |
| Skedar Ruins - Battle Shrine | 1:10 | 1:26 | 1:36 |
| Mr. Blonde's Revenge | 1:23 | 1:24 | 1:29 |
| Maian SOS | 1:38 | 1:54 | 2:11 |
| WAR! | 0:26 | 0:46 | 0:56 |
| The Duel | 0:03 | 0:06 | 0:09 |
| Totals | 24:01 | 33:13 | 39:07 |
Overall Combined Time: 1:36:21