Mercury Rising (1998) on Netflix

The NSA has developed what they believe is an unbreakable code which they call MERCURY. Now they ran a test to see if anyone can decipher the code by putting it in a puzzle magazine. Now Simon Lynch, an autistic boy who has an affinity for puzzles sees it and deciphers it and calls the NSA. Concerned the men in charge call their boss Kudrow and inform of what happened. Kudrow worried what might happen if this gets out orders that Simon be terminated. The man he sends kills his parents but is unable to find Simon and leaves when the police arrive. The police call the FBI to send someone to take a report of Simon who is missing and the man they send Art Jeffries is not exactly in good standing with the FBI because of an incident that occurred recently and is also not exactly OK because of the incident. Art finds Simon, who was hiding and takes him to the hospital. While there, the assassin takes another try but Art saves Simon and they go on the run.