The player steps into the role of Foxtrot 813, a Replica soldier under the direction of Paxton Fettel, the villain of the original game. Paxton turns against his fellow Replicas and attempts to reach ground zero of the nuclear blast set off by the F.E.A.R. Point Man's failed bid to contain Alma. She, however, is determined to stop Foxtrot 813, loosing her spectral creations against him.