The net is closing around Art and Simon when there is a warrant out for Art who is suspected of kidnapping the boy. With no one to trust and government assassins tracking them, Art befriends a girl in a coffee shop called Stacy to look after Simon as he meets with the lead code developer before he too is murdered in the street.
Art loses the assassin, but manages to get his hands on CCTV footage of the hitman. Using what he learnt from his short chat with the nerdy developer he talks again to his friend Tommy for support.
Meanwhile, the other nerdy developer is frightened for his life and uses a typewriter to tell the world about the crimes of his boss - Nick Kudrow (Alec Baldwin). He is soon taken out by the busy assassin, but leaves a carbon copy of his note in the bin to be found by his (also nerdy) girlfriend - the one who does the annoying Bart Simpson impression.
She takes the message to Tommy, and together they find Art in a bar. Tommy finally believes his friend, but tells him that they cannot take on the US Government. Art doesn't listen.
So they set a trap and Kudrow finds out that the boy is staying with Stacy and has someone pick them up. Art shows up with a SWAT team at the sky scraper Simon is taken to and they chase them a little, killing the assassin with bullets and broken glass. Outside Nick goes mental, telling Art that the code will save thousands of lives if they can just get rid of Simon.
He grabs Simon, looking to throw him off the edge, but Art shoots him in the chest. Nick then kindly pushes Simon away to safety a little in a terrible piece of acting as he has his eyes looking up in the "big death scene" type moment before he falls and crashes through a glass conservatory many floors below.
Later, Art checks up on Simon at school to learn that he has been adopted by another family. He was told by a doctor that Simon wouldn't recognise him, but wanted to stop by anyway. As it turns out, Simon knows that Art is a friend and gives him a hug.