One night in the pharmacy, Wesley is told by a mysterious woman named Fox that his recently murdered father was an assassin, and the killer, Cross, is now hunting him. Cross and Fox engage in a shoot-out followed by a car chase in the streets of Chicago. Wesley manages to escape and Fox has a shoot-out again with Cross, causing a car accident that knocks Wesley unconscious. Fox brings Wesley to the headquarters of the Fraternity, a thousand-year-old secret society of assassins. The group's current leader, Sloan, explains that Wesley's panic attacks are actually the untrained expression of a rare superhuman ability; when stressed, the drastically increased heart rate and adrenaline levels result in bursts of superhuman strength, speed, and reflexes. This claim is graphically demonstrated when he successfully shoots the wings off of three flies. The Fraternity can teach him to control this ability, so Wesley can follow in his father's footsteps as an assassin, beginning by inheriting his fortune. Wesley is initially reluctant and returns to work, only to finally snap when discovering several million dollars in his bank account. He excoriates his boss in front of the entire office, and on his way out, smashes Barry in the face with a computer keyboard. Fox is waiting outside to take him back to the Fraternity headquarters—an unassuming textile mill.
Wesley is then subjected to brutal training; among other forms of combat, he learns to fire bullets to curve around objects (even using Fox as a subject in front of the target). Afterward, Wesley is shown the Loom of Fate, a loom that gives the names of the targets through binary code hidden in weaving errors of the fabric. Those the Loom identifies will apparently cause tragedy in the future; but only Sloan sees and interprets the names Fate wishes to see dead. Wesley is initially reluctant about killing people. Then Fox reveals that in her childhood, a hired assassin burned her father alive in front of her—and said hitman was supposed to be killed by the Fraternity before that, but the assassin failed to pull the trigger. She now considers preventing such tragedies her mission in life along with her undying loyalty to the Loom of Fate and to the Fraternity.
After several routine missions and a chance meeting with Cross in which Wesley is shot in the arm with a deliberately traceable bullet, Sloan grants Wesley's wish to avenge his father and sends him after Cross—but then secretly gives Fox a mission to kill Wesley, saying that his name had come up in the Loom as well. Analyzing the bullet that hit Wesley, it is discovered that the manufacturer was Pekwarsky, a bullet-maker living in eastern Moravia, the birthplace of the Fraternity. Wesley and Fox travel there and capture Pekwarsky who then arranges a meeting with Cross. Wesley faces Cross alone on a moving train. Fox steals a car and crashes it into the train, eventually causing a derailment. After Cross saves Wesley's life by preventing him from falling into a ravine, Wesley fatally shoots him. Before dying, Cross reveals that he is Wesley's real father. Fox confirms this, and explains that Wesley was recruited because he was the only person that Cross would not kill. Fox then reveals the kill order on Wesley and raises her gun, but Wesley escapes by shooting out the glass underneath him and plunging into the river below with Cross's body.
Wesley is retrieved by Pekwarsky who takes him to his father's apartment that is located across the street from Wesley's old home. Pekwarsky explains that Sloan started manufacturing targets for profit after discovering that he was targeted by the Loom of Fate, and did not tell the Fraternity members that they were now nothing more than paid killers. Cross discovered the truth and went rogue and started killing Fraternity members to keep them away from his son. Pekwarsky departs, stating that Wesley's father wished him a life free of violence. Wesley, however, decides to take out Sloan after discovering a secret room containing all of his father's weapons and maps.
Wesley then goes to the grocery store to buy all the peanut butter they have. He then acquires an old garbage truck. Wesley mixes the peanut butter with a barrel of Astrolite G his father had to make a soft, melted peanut-buttery mixture which he then takes to the dump. Wesley carefully pours it down a tube where it makes a path into the garbage truck. Rats then sniff out the smell of peanut butter, and then follow it into the garbage truck. Wesley attaches an electric detonator made from digital watches onto each and every rat now stuffed with liquid explosive and puts them back in the truck. Wesley then uses the explosive rats to breach the Fraternity's fortress.
An enraged Wesley then assaults the inside of the Fraternity's textile mill-fortress and battles his way through it, killing nearly every Fraternity member in the process. Upon entering Sloan's office, he reveals Sloan's deception to the master assassins present in the room. Sloan reveals that all of their names had come up in the weaving, and that he had merely acted to protect them. Were they to follow the code, every one of them would be required to kill himself on the spot. Fox, who believes in the code more than anyone due to her own experience, turns on her fellow assassins and curves a bullet that kills every Fraternity member in the room, including herself, but not before she throws her gun to Wesley to distract him from trying to save her. During all of this mayhem the Loom of Fate is destroyed, and Sloan manages to escape.
Wesley, penniless once again, is left aimless. A man is then seen at a computer like Wesley was at the beginning of the film. Sloan appears and points a gun at the back of the man's head. At that moment the man turns around and is revealed to be a decoy. Sloan is then killed by Wesley using a long-distance bullet. Similar to in the comic book miniseries, the film ends with Wesley stating his accomplishments and then breaking the fourth wall by asking the audience, "What the fuck have you done lately?"