The first game opens with Paxton Fettel taking command of a battalion of Replica Soldiers and storming the Armacham Technology Corporation (ATC) headquarters. Surveillance footage shows Fettel in the act of cannibalizing one of his victims.
You, the player, are introduced as the new "Point Man" for the First Encounter Assault Recon team, a secret government organization that specializes in dealing with paranormal threats. The team coordinator, Rowdy Betters, introduces you to teammates Spen Jankowski and Jin Sun-Kwon. The team is ordered to eliminate Fettel. As a failsafe measure, ATC implanted all bioengineered soldiers with a honing device, so the team is able to track Fettel's movements with the Hannibal-3 spy satellite.
The search for Paxton Fettel begins at an abandoned building in Auburn. While searching the premises, Fettel ambushes you and before losing consciousness Fettel enigmatically says "they all deserve to die."
Fettel's signal is lost. In the meantime, you and the SFOD-D squad are ordered to investigate a group of Replica soldiers at the Sullivan Shipping and receiving facility. The SFOD-D team is mysteriously massacred and you are nearly killed by an explosion triggered by the apparition of a little girl in a red dress, Alma.
The search for Fettel continues to the adjacent South River Wastewater Treatment Plant and on to ATC headquarters. While Fettel evades the team, you experience increasingly disturbing visions and hallucinations of Fettel and Alma. Through hallucinations, hacked laptops and hints from other characters, the story unfolds. You learn that Fettel is the offspring of Alma, the result of her being forcibly impregnated with a genetically modified embryo. You also discover that Fettel is the younger of two brothers produced by the Origin program.
ATC
The pursuit of Fettel leads the team to the underground Origin facility that was closed down by ATC when Alma grew too powerful to contain. The team must now fight both Replica soldiers and ATC guards who have been ordered to cover up the affair.
You finally confront Fettel, which triggers a hallucination where you learn that YOU are the second of Alma's sons. After the hallucination ends you must do the inevitable and kill your brother, Fettel.
Fettel fails to release Alma but Harlan Wade persists in trying to free her. Harlan Wade, the architect of the Origin project, frees Alma out of guilt for the suffering that he has caused her. Upon her release, Alma immediately kills him. Alma's liberation triggers nightmares that break through from your hallucinations to the real world, and visions of an older Alma stalk you through the underground facility.
You must race to destroy the facility by knocking out the energy pylons which will start a chain reaction and cause a critical meltdown in the facility. As you flee, a vision comes through in which the horrific fact that Harlan Wade was Alma's father is revealed.
You escape the facility in time to see an enormous explosion that knocks you unconscious. When you come to, you find yourself in a helicopter with the SFOD-D Leader Douglas Holiday and Jin overlooking a mushroom cloud billowing out of an urban setting. The Origin facility has been destroyed, but Alma has been released and there is no telling what form her rage will take now that she is free.
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