| Stage | Agent | Special Agent | Perfect Agent | Total |
| dataDyne Central - Defection | 100 | 31 | 55 | 186 |
| dataDyne Research - Investigation | 76 | 63 | 83 | 222 |
| dataDyne Central - Extraction | 82 | 78 | 60 | 220 |
| Carrington Villa - Hostage One | 83 | 79 | 88 | 250 |
| Chicago - Stealth | 80 | 60 | 49 | 189 |
| G5 Building - Reconnaissance | 67 | 70 | 63 | 200 |
| Area 51 - Infiltration | 79 | 69 | 84 | 232 |
| Area 51 - Rescue | 81 | 81 | 84 | 246 |
| Area 51 - Escape | 86 | 84 | 86 | 256 |
| Air Base - Espionage | 72 | 63 | 75 | 210 |
| Air Force One - Antiterrorism | 76 | 40 | 83 | 199 |
| Crash Site - Confrontation | 41 | 46 | 62 | 149 |
| Pelagic II - Exploration | 76 | 82 | 81 | 239 |
| Deep Sea - Nullify Threat | 88 | 92 | 91 | 271 |
| Carrington Institute - Defense | 78 | 60 | 60 | 198 |
| Attack Ship - Covert Assault | 51 | 67 | 70 | 188 |
| Skedar Ruins - Battle Shrine | 73 | 70 | 77 | 220 |
| Mr. Blonde's Revenge | 83 | 83 | 82 | 248 |
| Maian SOS | 88 | 54 | 72 | 214 |
| WAR! | 48 | 65 | 68 | 181 |
| The Duel | 100 | 100 | 100 | 300 |
| Total Points | 1608 | 1437 | 1573 | 4618 |