Plot
The film opens with a bank robbery hostage crisis in South Dakota. Undercover as one of the criminals, FBI agent Art Jeffries guards fourteen year old James while trying to convince the gang’s leader, Edgar Halstrom, to surrender. Despite pleading for more time to negotiate, an armed FBI task force storms the building, fatally shooting both James and the thieves. Art confronts his superior Hartley, punching him when the latter says they must answer to Washington. As a result of his outburst, Jeffries is demoted to desk duty.
Years later, a nine-year-old autistic savant named Simon Lynch is given a sophisticated puzzle book by his teacher. Simon quickly solves a particular puzzle and phones a number encoded in the solution. This call reaches two National Security Agency cryptographers, Dean Crandell and Leo Pedranski, who created the new cypher Simon has cracked. Pedranski and Crandell report the situation to their boss, Lieutenant Colonel Nick Kudrow, who severely rebukes the pair for their unauthorized actions, describing Simon and his abilities as a national security threat. Two assassins, Peter Burrell and Shayes, are sent by Kudrow to terminate the boy and his parents, Martin and Jenny.
Posing as a police detective, Burrell murders both Simon's mother and father, but is unable to find Simon himself. Upon finding that Martin dialed 911 before he died, Burrell stages a murder/suicide between him and his wife Jenny before exiting the Lynch residence. Shayes serves as his getaway driver.
Jeffries is sent to investigate the crime scene and finds Simon in a hidden crawl space in his bedroom closet. Simon is taken to a protection ward at the hospital, where a nurse explains the nature of Simon's autism to Art, and why he cannot be interrogated. Burrell impersonates a doctor and makes another attempt on Simon's life. Art saves Simon and flees the premises, and tries unsuccessfully to convince Simon that he is a friend instead of a stranger. Later, while on a train, Shayes tries to kill Simon, but Art intervenes, knocking him off the train and onto the tracks as another locomotive passes, killing him.
Under Kudrow's direction, the NSA frames Art as Simon's kidnapper. However, fellow agent and friend Tommy Jordan does not believe the story and assists Art, who borrows Jordan's car and takes Simon back to his house. Simon again calls the telephone number written into the code and Art is able to talk to Crandell and Pedranski. As Crandell arranges a meeting at the Wrigley Building by the next morning, Art goes to the meeting, leaving Simon under the care of a woman in a coffee shop, Stacey Siebring, who later agrees to help Art take care of Simon. Crandell tells Jeffries about Mercury and Kudrow, but is shot dead by Burrell before he can reveal everything.
Pedranski, having learned Crandell's fate, tries to reveal Kudrow's unlawful actions by writing letters on a typewriter: one to Art and a carbon copy for the Senate Oversight Committee, but Burrell tracks Pedranski down and kills him as well, confiscating the letters. However, the assassin overlooks Pedranski's carbon copies, which his girlfriend, NSA analyst Emily Lang, takes to the FBI. Jordan discreetly arranges for her to meet with Art to show them the carbon copies; covered in Pedranski’s fingerprints, they become crucial evidence. Art then goes to Kudrow’s home during his birthday party, confronting him in his wine cellar. He berates the NSA head for targeting Simon, demands that Kudrow announce on national TV that the Mercury Encryption Project is a failure, and kicks him for trying to justify his crimes on grounds of protecting American spies.
Under Art's suggestion, Jordan arranges for Simon to go into the Witness Protection Program, but Kudrow, unwilling to reveal his failure and determined to kill Simon, forcibly takes charge of the Witness Protection while revealing to Lomax, the FBI Special Agent in charge, that Jordan forged the witness protection documents. However, unknown to Kudrow, Tommy shows the carbon paper evidence to Lomax and confirms that the fingerprint markings on it were Pedranski's, validating the evidence against Kudrow. Stacey and Simon leave for the pick-up point at the top of a skyscraper, where Kudrow and Burrell prepare to take Simon away on a helicopter, but Jeffries, with Jordan and an FBI task force's help, sets a trap at the meeting spot. A gunfight ensues between Burrell and the FBI, ending with Burrell being fatally slashed by glass shards when plexiglass windows are blown inward, while Art fights Kudrow one-on-one, and Simon assists him by retrieving his gun. Kudrow attempts to throw Simon off the roof, but Jeffries shoots him multiple times, and he falls off the edge and to his death.
Art and Siebring later visit Simon, now living with foster parents, at his school. Simon embraces Art as a welcome friend, having accepted him as a person he trusts.
