The story of F.E.A.R. is presented in such a way that only a few minor elements are presented in the game's beginning, thus allowing players to experience the adventure as an unfolding storyline that becomes further tied to the nameless Point Man as time goes on.The manual briefly mentions the player character's recent induction as "Point Man" to F.E.A.R. (First Encounter Assault Recon), a secret special ops group of the U.S. government specialized in dealing with paranormal threats. The character's extraordinarily quick reflexes are described as well, hinting that the government is interested in his abilities.
During the course of the game, the player interacts with a number of different characters from various organizations. Some of them are allies, such as the F.E.A.R. and Delta Force team members, while others are hostile, such as Fettel's replica soldiers and some ATC (Armacham Technology Corporation) personnel. The player's character never speaks, and instead participates in one-sided discussions with other characters. On occasion your character, the Point Man, is required to hand a communicator to other characters, allowing them to speak over the F.E.A.R. team radio. No artificial intelligence-controlled characters fight alongside the player in F.E.A.R., except for some sequences in the expansions Extraction Point and Perseus Mandate.
When the game begins, the player witnesses a man named Paxton Fettel taking command of a battalion of telepathically controlled clone supersoldiers, seizing control of Armacham Technology Corporation (ATC) headquarters, and killing all its occupants.
Now fully in control of the Point Man, the player attends a briefing held by Commissioner Rowdy Betters, in the company of his F.E.A.R. team-mates Spen Jankowski and Jin Sun-Kwon. The team's mission is to eliminate Fettel, operating in conjunction with Delta Force, a strike team assigned to assist Point Man.
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 revolve around a red-dressed little girl named Alma. 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 (Which will be explained later) and the existence of another child of Alma, who was born before Fettel.
All clues lead F.E.A.R. to believe Fettel is under control of 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. The story does not end here, however, as Alma is nonetheless freed when her storage chamber is opened by ATC researcher and leader of Project Origin, Harlan Wade, who felt guilty over the company's treatment of Alma and who actually was her father. The player is then called to sabotage the structure's reactor, running a gauntlet against Alma's demonic appiritions before the whole location explodes. In the aftermath of the detonation, a Delta Force Black Hawk helicopter extracts the Point Man from the rubble, rescuing him. While the player and the survivors of the F.E.A.R team survey the results of the explosion from the helicopter, Alma makes one last sudden appearance over the side of the helicopter, preparing to pull herself up into the cabin: the destruction of the Origin facility has not stopped her quest for revenge.
After the game's credits, the player can listen to a phone call between a mysterious senator and ATC president Genovieve Aristide, which offers some further explanation: the woman considers the project under control and deems the "first prototype" (presumably a reference to the point-man) a success.