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