| Stage | Agent | Special Agent | Perfect Agent |
| dataDyne Central- Defection | 0:06 | 0:38 | 1:37 |
| dataDyne Research- Investigation | 1:31 | 2:17 | 3:31 |
| dataDyne Central- Extraction | 0:53 | 1:37 | 1:48 |
| Carrington Villa- Hostage One | 1:14 | 1:33 | 1:49 |
| Chicago- Stealth | 0:16 | 0:29 | 0:31 |
| G5 Building- Reconnaissance | 0:47 | 0:55 | 1:08 |
| Area 51- Infiltration | 1:13 | 1:52 | 3:06 |
| Aera 51- Rescue | 1:31 | 2:28 | 3:23 |
| Area 51- Escape | 2:37 | 3:50 | 3:51 |
| Air Base- Espionage | 1:18 | 1:49 | 2:29 |
| Air Force One- Antiterrorism | 0:57 | 1:27 | 1:32 |
| Crash Site- Confrontation | 1:22 | 1:32 | 2:15 |
| Pelagic II- Exploration | 0:59 | 2:05 | 2:35 |
| Deep Sea- Nullify Threat | 3:20 | 4:53 | 4:17 |
| Carrington Institute- Defense | 0:53 | 1:32 | 2:04 |
| Attack Ship- Cover Assault | 2:28 | 2:55 | 4:17 |
| Skedar Ruins- Battle Shrine | 1:14 | 1:27 | 1:36 |
| Mr.Blonde's Revenge | 1:36 | 1:36 | 1:39 |
| Maian SOS | 1:46 | 2:12 | 2:20 |
| WAR! | 0:26 | 0:50 | 1:01 |
| The Duel | 0:03 | 0:06 | 0:10 |
| Total Time | 26:30 | 38:03 | 46:59 |