The main character is Alex Mercer, who is a genetically mutated shape-shifter with no memory of his past. He is hell bent on trying to regain his memory and find out what has happened to him. He breaks out of the lab that he woke up in and starts roaming the streets of New York to find his past. His efforts are hindered somewhat, however, due to a strange virus that has been spreading throughout the city, possibly from the same lab he left. The citizens in some infected areas of the city have been mutated into monsters by this strange virus and the military has been sent in to handle the situation. Project Blackwatch, an elite branch of the military who deals with biological outbreaks, is also sent in to help contain the outbreak. Alex fights both of these groups and searches for information about Project Blackwatch, which he believes is behind both the virus and his new powers. The developers specify that Alex does not kill infected or soldiers because he wants to save New York or stop the corrupt military, but merely because he wants to uncover the secrets of his past.