The first in the series, players control Alex Mercer, a powerful and deadly shape shifter with no memories of his past. Alex hunts those he thinks are responsible for his fate with the help of his sister, Dana Mercer. Along with Mercer, a deadly virus threatens the existence of the citizens. Mercer is later aided by Bradley Ragland in his search for the truth. Mercer realizes that he was responsible for the viral outbreak in Manhattan. In order to save the city from being destroyed by Blackwatch, a shady military organization determined to stop the spread of virus and Mercer, Alex allies himself with Robert Cross who was part of Blackwatch. Mercer succeeds in saving the city from destruction, but becomes a ghost among its people.