In 2008, a viral outbreak caused by Alex Mercer and further spread by Elizabeth Greene, ravaged the once relatively safe island. The citizens infected with the virus were mutated into mindless creatures who served Greene's purpose of spreading the virus.
In order to contain the infection, martial law was implemented on the island and the local Police were replaced with Marine forces. While the Marines were the public face, a black ops military unit Blackwatch operated within the city. However, the city was deteriorating fast while Blackwatch tried to capture Alex Mercer and Elizabeth Greene.
Blackwatch established their base of command (call sign Red Crown) at the island's port, while the Marines operating within the city managed to setup temporary bases using the existing buildings. However, there were constant battles between the military and infected forces.
After Greene's escape from Gentek, infected Hives were seen across the city. These Hives increased the rate of infection within its vicinity. Eventually, the infected population had increased to cover 80% of the island. Upon Greene's death, the infected population was drastically reduced and in the following weeks, the city had returned to normality.
For over a year, the populace assumed the viral outbreak had been completely cleansed. However, Alex Mercer returned to the city with the intention of ushering a new age, and Manhattan was to be the first city to fall under the new regime. Mercer returned to Penn station, the place where his death had occurred and he had become a host for the Blacklight virus and unleashed the virus once more.
For the next two months, Blackwatch was unable to control the infection which led to the zone being quarantined by the destruction of all bridges and presumably tunnels. With Blackwatch and Gentek experimenting on the citizens of New York, the city was split into three zones, and Manhattan Island was designated as the Red Zone. Blackwatch knew that this was the new home of Alex Mercer and suspected that he was behind the outbreak.
The city was completely devastated, with most of the buildings either partially or entirely demolished and tilted. Large tentacle-like appendages held what was left of most buildings, and fires burned endlessly while the streets were littered with bodies of Blackwatch soldiers and Marines who were sent in as strike squads. The constant struggle between the military and the infected remained constant. A few uninfected civilians still existed, often either finding shelter near Blackwatch bases or hiding in buildings or on rooftops.