NOTE: This catch-up is full of SPOILER!s. and takes into account that you already know everybody and everything's names.

The game starts out with a cutscene that shows Alma presumably taking control of Paxton Fettel and a group of telepathically controlled cloned supersoldiers. He then procedes to kill every single person in Armacham Technology Corp. (ATC) Headquarters. You then proceed to hear a phone call between ATC president Aristide and an unknown senator, stating the "Origin" has had an uprising, informing the player that "Fettel has taken over the prototypes."

The game then gives you control of the "point man", who is described to have "reflexes off of the charts" both in-game and in the manual, and set in the briefing room for F.E.A.R. being attented by Commissioner Betters, and the F.E.A.R. team Jankowski and Jin Sun-Kwon. Your mission objective is to eliminate Fettel, who, as the info states, is a psychopathic commander. After the cutscene ends, you will have a hallucination showing Fettel asking you, "What's the first thing you remember?". and someone saying, "You will be a god among man."

As you progress through the game, you will have MANY more hallucinations that focus around the creepiness of Alma and how she seems to be able to kill people with her mind, messages going through your mind hinting of that "you were born here". Throughout the game Fettel himself gives you many cryptic messages, and you also find many laptops throughout the mission, learning many details describing "Project Origin"; how Fettel is the son of Alma, how he is a powerful psychic, and that there is another child, born before Alma. There are also a few very cinematic in-game cutscenes of Alma appearing herself, such as trying to escape and exploding hallway with her walking towards you, and when you encounter a small child in the sewers that always seems to escape your view.

All the hints in the game and quotes from Betters lead you to believe that Alma has taken control of Fettel, who was securely kept in the Origin facility when ATC closed the project because of the believed danger the woman posed. You also start to encounter ATC soldiers, who have appeared because of orders to cover the Project. Later in the game, once you encounter Fettel himself, you learn that YOU are the first son of Alma, and you are given control to kill Fettel. You learn that the father of Alma, Harlan Wade, leader of project Origin, freed Alma himself because he felt guilty giving his 8-year-old daughter to the project. After sabotaging the whole facility to blow, you escape on a helicopter, but not right before the game ends do you seem Alma over side the helicopter about to-