Someone knows too much.

While exploring the scene of the murders at a modest Chicago home, Jeffries discovers the missing boy hidden in a crawl space. The autistic child, Simon (Miko Hughes), is deeply traumatized and unable to speak, and the hard-edged agent immediately feels an intuitive connection with the boy's pain and isolation. His cop instincts also tell him that the boy is in danger, prompting him to demand police surveillance at the hospital where Simon is being cared for. When the surveillance is inexplicably dropped, Jeffries takes the boy under his own protection and flees.

Although his associates disregard Jeffries' accusations, chalking them up to his paranoia, an attack on Simon proves Jeffries' theory. Simon, who is a savant, a condition not uncommon in people with autism, has, in fact, become the target of ruthless assassins after inadvertently deciphering a top-secret military code, Mercury. This code serves to protect American espionage operations around the world and was thought to be infallible and indecipherable. The two fugitives are now on a collision course with the most powerful and covert government force in the United States - the omnipotent and elusive National Security Agency (NSA) led by high-ranking NSA official, Lt. Colonel Nicholas Kudrow (Alec Baldwin), determined to use whatever means necessary to protect the code on which he has staked his career and made a name for himself. Moreover, he will not let himself or the code be taken down by a 9-year-old autistic child.

Now outcast from the FBI and unable to seek help from the police, Jeffries and Simon are alone, in peril and on the run.