| Stage | Agent | Special Agent | Perfect Agent | Total |
| dataDyne Central - Defection | 19 | 35 | 57 | 111 |
| dataDyne Research - Investigation | 26 | 60 | 35 | 121 |
| dataDyne Central - Extraction | 67 | 31 | 46 | 144 |
| Carrington Villa - Hostage One | 75 | 75 | 52 | 202 |
| Chicago - Stealth | 86 | 63 | 54 | 203 |
| G5 Building - Reconnaissance | 71 | 73 | 66 | 210 |
| Area 51 - Infiltration | 4 | 45 | 20 | 69 |
| Area 51 - Rescue | 67 | 60 | 59 | 186 |
| Area 51 - Escape | 60 | 34 | 38 | 132 |
| Air Base - Espionage | 36 | 37 | 62 | 135 |
| Air Force One - Antiterrorism | 26 | 44 | 64 | 134 |
| Crash Site - Confrontation | 44 | 50 | 64 | 158 |
| Pelagic II - Exploration | 60 | 58 | 31 | 149 |
| Deep Sea - Nullify Threat | 83 | 83 | 54 | 220 |
| Carrington Institute - Defense | 33 | 66 | 44 | 143 |
| Attack Ship - Covert Assault | 0 | 44 | 47 | 91 |
| Skedar Ruins - Battle Shrine | 57 | 56 | 62 | 175 |
| Mr. Blonde's Revenge | 18 | 38 | 53 | 109 |
| Maian SOS | 75 | 58 | 36 | 169 |
| WAR! | 51 | 46 | 52 | 149 |
| The Duel | 100 | 100 | 64 | 267 |
| Total Points | 1058 | 1156 | 1060 | 3274 |