Here is the full list of all 41 Prototype trophies - there are 26 bronze, 10 silver, 4 gold and 1 platinum.
Obtain all trophies.
Complete 3 missions without causing a single Military Alert.
Kill 53,596 infected.
Acquire all nodes of the Web of Intrigue.
Discover the history of Elizabeth Greene through the Web of Intrigue.
Complete Story Mode on hard difficulty.
Collect all Landmark collectibles scattered across New York City.
Collect all Hint Collectibles scattered across New York City.
Shoot down 50 helicopters while driving armor.
Run over 500 characters in a single tank.
Destroy 25 strike teams.
Destroy 25 Infected Water Towers before they hatch.
Achieve a Platinum Medal in all Events.
Discover the truth behind Hope, Idaho through the Web of Intrigue.
Discover what happened to Alex Mercer through the Web of Intrigue.
Complete all Consume Events.
Patsy 5 military personnel.
Acquire all available upgrades.
Achieve a rating of Gold or better in all Events.
Destroy 2,000 vehicles.
Destroy 20 Helicopters in a single Helicopter flight.
Complete the game while consuming 10 Civilians or fewer.
Complete Story Mode in any difficulty without dying.
Complete the Supreme Hybrid Boss Battle.
Seize 50 vehicles from enemy hands.
Evade 10 strike teams.
Complete the Mother Boss Battle.
Catch any object tossed by a Hydra; and throw it back.
Kill 50 characters in 5 seconds.
Destroy 10 Military Bases or Infected Hives in New York City.
Kill 15 characters with a single Whipfist attack.
Complete the Supreme Hunter Boss Battle.
Consume 200 characters to boost your health.
Consume 50 Web Targets.
Infiltrate 10 Military Bases disguised as a Commander.
Complete a mission without causing a single Military Alert.
Gain the ability to drive and fly all vehicles.
Complete the Specialist Boss Fight.
Complete the Hunter Boss Encounter.
Use the Upgrade Menu to acquire an Upgrade.
Unlock the Web of Intrigue.