It took a bit to remember the title, ( I had to IMDB it) but “Mercury Rising” from 1998 comes to mind. Bruce Willis plays the part of an FBI agent protecting a 9 year-old autistic boy from the NSA assassins. The NSA had published “Mercury”, their newest secret code, as a test, in puzzle magazines in the belief that it could not be broken. When Simon, a 9 year-old boy, reads the code and follows the instructions encrypted within a puzzle, he calls the NSA on the phone, and they freak out. The head of the department decides Simon needs to be eliminated, and it becomes the job of the FBI agent to protect Simon and expose the abuse of power by a government agency.