ust after ATC murders Aldus Bishop and openly begins to battle against F.E.A.R. and Delta Force, Commander Betters airdrops a second F.E.A.R. team to ATC's secondary facility to investigate the company and any wrongdoing it is involved with. This second F.E.A.R. team consists of Captain David Raynes, Lt. Steve Chen, and the unnamed F.E.A.R. Sergeant (the player character). After battling through Replica soldiers and ATC security forces, the second F.E.A.R. team discover that a third faction has already infiltrated the ATC facility and killed everyone inside. This faction consists of highly trained mercenaries known as "Nightcrawlers", who are armed with advanced weapons. The Nightcrawler ranks also include several elite super-soldiers who possess the same SloMo ability previously demonstrated by the F.E.A.R. Pointman.

It is revealed that the Nightcrawlers work for the mysterious Senator, and are searching for "the Source", the genetic template from which the Replica soldiers were created (later revealed to be a sample of Paxton Fettel's DNA). The F.E.A.R. team discover that Armacham had 3 major facilities involved in Project Perseus; an active bio-research facility where Fettel's DNA is stored, an abandoned secret cloning facility where the Replica soldiers were actually produced, and the Origin facility where Alma is imprisoned. F.E.A.R. and Delta Force launch an assault against the bio-research facility, battling through Replica, ATC, and Nightcrawler forces. However, the Nightcrawlers manage to obtain and escape with a sample of Fettel's DNA. The F.E.A.R. team almost manages to capture Gavin Morrison, the Senator's main agent, but are interrupted by the explosion of the Origin facility, which throws the entire city into chaos.