During the Credits
Audio clips of citizens, military officials and the senator of New York discussing the events that took place during the game can be heard during the credits of Prototype. There are also black and red images of New York in ruins and characters from the game shown alongside the credits.
After the Credits (spoilers)
There is a scene showing Alex Mercer standing on top of a building and saying, “One virus. 3 weeks. Millions dead and I was there. My name is Alex Mercer and my work is almost done.” After the extra scene ‘Free Roam’ mode is activated allowing the the player to continue working towards getting rid of the infection in the city and building up their character’s skills by doing side missions.
One of the things a player can do after beating the game is continue consuming targets to unlock new web of intrigue cutscenes that go into more detail explaining the story. After all scientist have been consumed there is a secret cutscene unlocked that shows Alex finding Karen Parker, Alex’s former romantic interest, who betrayed him earlier in the game.
Alternate Ending (spoilers)
There is also an alternate ending if the last mission is failed which shows the bomb going off and annihilating New York City.