- FBI Agent Ethan Thomas is framed for the murder of a detective and officer. In order to uncover who murdered the two officers with his gun, he has to do whatever it takes and fight his way through violent, psychotic individuals.
- FBI Agent Ethan Thomas is called to a crime scene at a disused office block, he investigates the scene with Agent Dickenson and Officer Becker. The crime is the murder of a young woman, placed with a male department store mannequin, here the player is given a tutorial from Lieutenant Rosa, Ethan discovers several clues tying to the motif of a known serial killer, the Match Maker. The woman has been strangled, there's a right hand print on her neck with the index finger missing and the mannequin has scarring on the left side of its face. No mugshots of the Match Maker exist, but Thomas suggests he has the same facial scarring..
Dickenson can smell cigarette smoke and searches a nearby office, a person can be heard running around on the fire escape, it's believed to be the suspect, backup is called, Dickenson and Becker follow up the fire escape, Thomas investigates the building, fighting off violent squatters and collecting dead birds and metal pieces. Thomas reactivates the building's power at a junction box and the blast knocks him back and his gun out of his hand. The suspect steals the gun, Thomas has to fight through the office with melee weapons taken from the environment. Eventually the suspect jumps Thomas and holds his gun at him, telling him they are both on the same path of righteousness, when Dickenson and Becker enter the suspect shoots them dead, then throws Thomas out of a window.
Thomas awakens in his apartment where an elderly man is watching over him. He is Malcolm Vanhorn, a family friend, he found Thomas lying in the street and brought him home. Thomas is suspected to have killed the two officers and the police are en route, Malcolm helps him escape and tells him to go to the train station. From this point Thomas' only allies are Rosa and Malcolm, Malcolm makes reference to Thomas having some incredible instincts that have made him a successful agent, Rosa analyzes any evidence found. Thomas finds a dark room opposite his apartment containing photos of himself and newspaper clippings of serial murders. Thomas continues chasing the suspect through the underground metro and finds more clues in the suspect's hideout, two highlighted areas on a metro line map and some mannequin parts, the parts lead to Bart's Department Store, a shopping mall closed in 1991.
On the ride there Thomas receives a call from his superior Director Farrell, Farrell is certain that Thomas killed the officers, Thomas argues otherwise and refuses psychiatric help, yet he experiences a mirage and questions his sanity. Once at the store Thomas finds the trail of another murder, deep in the backrooms is a Match Maker crime scene, albeit with a male victim and female mannequin. An examination of the body reveals facial scarring and a missing right index finger, the deceased is the Match Maker serial killer. Rosa analyzes a chemical compound on the Match Maker's neck, furthermore from the newspaper clippings found in the dark room Rosa sees a connection, all the murderers were cases that Thomas worked on, all cases went cold when the killing suddenly stopped. It's theorized the last victims of each case were the killers themselves murdered in their methods, only one killer is still active, the Torturer.
The police have traced Thomas to the mall and he escapes, he recaps on all information so far. The person that attacked Thomas in the office is also the one targeting serial killers, under the name Serial Killer X. Thomas is to find the Torturer before X gets to him, Rosa instructs Thomas to meet her at the library, which is closed for renovation after a fire.
Thomas meets Rosa who has his file with her, there are curious details about Thomas, being physically stronger than most humans, an odd addition in the brain and a chest x-ray with the vocal cords blacked out and a citation to a highly classified file. Thomas experiences more mirages while searching for a working computer, a computer is accessed but the network is lost, Rosa is captured and Thomas finds her elsewhere. X captured her and made her search for information regarding the Torturer, his name is Carl Anderson, a student of St Joseph's for the Troubled, closed in 2000, a former gym teacher working there, Samuel Tibbits reported that Anderson had fantasies that matched the Torturer's methods and now Tibbits has disappeared. Thomas heads there next, Malcolm is there asking of Thomas' investigation, Thomas finds his presence there questionable.
Thomas finds organic matter belonging to Tibbits and eventually him, the Torturer got to him, before he dies he says that another man captured the Torturer. Rosa reports the chemical compound found on the Match Maker is from a pesticide used by an apple orchard ruined by a maggot outbreak, Thomas makes to leave and has another violent hallucination, he recovers and finds Malcolm outside.
The two drive to the orchard, Thomas uncovers writing on the walls telling a cryptic clue. "The dark path to righteousness is beyond which you see yourself to be." This clue leads him to a secret room hidden behind a mirror in the basement, where X has keeping details on Thomas' career. A noise from upstairs draws Thomas' attention, a man has committed suicide in the bedrooms, analysis of his fingerprints verify that this is the Torturer.
Farrell interrupts their call and terminates Thomas' lab access, then X enters the building, Thomas waits for him to enter and jumps him, he chases X through the house until he's knocked out by Malcolm. X is his nephew, Leeland, he tries talking sense into him only for Leeland to strangle him.
Thomas awakens in the orchard stables, tied to the wall, Malcolm is unconscious on the floor, Leeland explains that he had been manipulating Thomas, observing his progress to find the killers and kill them, then cuts off Thomas' left index finger like the Match Maker. Malcolm recovers and restrains Leeland, Thomas escapes to find the source of the madness in the city, a humanoid creature known as "the Hate" Thomas fights him in one-on-one combat and kills him. Malcolm drives Thomas home, but Leeland is held in the trunk, Thomas orders the vehicle pulled over and finds Leeland tied up, Thomas wishes to kill him for what he went through, Malcolm says he's not in his right mind, the Hate had gotten to him as well. The player can then choose to shoot Leeland or spare him, whereupon Leeland will shoot himself.
Thomas meets Rosa at a diner, depending on how many metal pieces were found in the game, Rosa can give more detail on the cause of the insanity, Thomas asks if he can trust her, she leaves a written note saying she's wearing a wire. Thomas then goes to the bathroom and experiences another hallucination, of the Hate appearing behind him and his own mouth becoming full of metal pieces like theirs.
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