It is later revealed that Alex Mercer, having access to a sample of the virus which was being researched at GENTEK, was the one who released the virus in New York. Subsequently being shot dead by Blackwatch agents, he is then delivered to the morgue where he awakens at the start of the game. However, when he was shot and killed the virus he had released found its way into his body thus became infected. After he became infected the virus took over his body and the character you play is in fact the virus itself and not Alex Mercer. The virus had copied him so well (down to a genetic level), it didn't even know it wasn't the real Alex.