What's the name of this movie?

I'm not exactly sure all the events but I believe this movie came out somewhere between 2000-2010. It's about a secret agent whom the FBI/CIA consider have gone rogue because he kidnapped a teenager who invented a device (not sure what it was). But the agent was actually protecting the kid and hid him in some location. When he went back for the kid in some sort of room he wasn't there but the kid had etched on the walls a message where to find him. Another scene in the movie is where the agent and a girl is in a hotel room and the girl pushes the pen that the FBI gave her to signal them that he was there but he jumps into a river? and they can't find his body.