Fettel is located by means of a satellite tracking device and hunted by F.E.A.R. and Delta Force over several locations. While the villain evades capture by the special forces, the player witnesses unexplained, and occasionally life-threatening, paranormal phenomena, including hallucinations that frequently afflict him, all of which are centered on a red-dressed little girl named Alma (Melissa Roberts). Laptops found in the course of the mission, remotely hacked by Commissioner Betters, provide details regarding the background story; the player learns how Fettel was raised to become a telepathic military commander, that he is the son of Alma, who is described as being a powerful psychic as part of Project Origin

All clues lead F.E.A.R. to believe Fettel is being controlled by Alma, who was locked in the Origin facility when ATC closed down the project owing to the danger the woman posed; Fettel is searching for that same facility to free his mother. The player takes the Point Man to the abandoned structure, fighting back both the clone soldiers and ATC guards, who have received orders to cover up the whole affair. When the protagonist comes to finally face Fettel, he is drawn into a hallucination where the player learns how the Point Man is Alma's first son and is thereafter enabled to kill Fettel himself