Just 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 Wade'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 Wade'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.
The Sergeant and Lt. Chen awake in an abandoned part of the city's subway system, and discover that the explosion of the Origin facility has unleashed a wave of deadly paranormal activity. Chen manages to fight off an attack initially (the same creatures that killed Douglas Holiday), but is torn to pieces by a new type of Alma apparition that comes out of the floor. The Sergeant continues through the subway system in pursuit of the Nightcrawlers. The Sergeant eventually manages to reach the surface, and reestablishes contact with Captain Raynes, who orders him to make his way to the ATC Cloning Facility, where the Nightcrawlers seem to be headed. This is complicated by the re-activation of the Replica soldiers following Fettel's resurrection.
On the way to the Cloning Facility, the Sergeant encounters Gavin Morrison, who has been captured by the Nightcrawlers. Morrison reveals that the Nightcrawlers are attempting to acquire a sample of Alma's DNA, and that they must be stopped. Morrison briefly accompanies the Sergeant on the way to the Cloning Facility, but is killed when Alma causes an armored car to drop on him.
The Sergeant eventually reaches the Cloning Facility, where he is greeted by the ghost of Paxton Fettel, who makes several cryptic communications with the Sergeant, as well as sending in Replica soldiers to kill him. The Sergeant fights his way through Fettel's Replicas as well as the Nightcrawler forces, but is too late to prevent the Nightcrawler Commander from acquiring a sample of Alma's DNA.
The Sergeant pursues the Nightcrawler Commander through the facility, eventually battling the Commander and the remaining Nightcrawler forces in a final showdown. The Sergeant then acquires the sample of Alma's DNA, and escapes to the surface where Captain Raynes is waiting for him. The Sergeant and Raynes fight their way through Fettel's final Replica Elite soldiers, and successfully manage to reach an evacuation helicopter. (The sky is the same at the end of the first expansion, it must be about twenty to thirty minutes before the next explosion.) When the Sergeant gets inside, Lt. Chen appears to be there waiting for them. Captain Raynes remarks that the Sergeant is due for a promotion to Lieutenant, and that Chen would be proud of him. Chen's ghost then fades away.
After the credits roll, a Nightcrawler Elite is seen approaching the Senator, bringing him the sample of Fettel's DNA. The Senator asks how many losses there were, and the Nightcrawler Elite replies that losses were "acceptable".
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