The player takes the role of Foxtrot 813, a Replica soldier guided by Paxton Fettel, the antagonist of the original game. Paxton turn on his fellow Replica and try to reach the epicentre of the nuclear explosion triggered by the F.E.A.R. Point Man's failed attempt to contain Alma. However she is striving to stop Foxtrot 813 by sending ghostly creations against him.