Nathan (Taylor Lautner) is a high schooler in Pennslyvania, who likes parties and boxing with his dad. He has rage and self-identity issues, and sees a shink (Sigourney Weaver). He's apparently a good wrestler as well as a kickboxer. He's assigned to work on a school project with his neighbor, Karen (Lily Collins), who he's sweet on, but too shy to talk to. They find a website for missing children, and, aging one online, see a likeness of Nathan. He contacts the site, and it triggers an alert in New York. The tech on duty (Nickola Shreli) in New York activates a trace and Nathan's webcam and send a photo of Nathan to a Mr Kozlow (Michael Nyqvist).
He takes some old pictures to his friend Gilly (Allen Williamson), who thinks they are suspicious. He confronts his mother (Maria Bello), who fortunately gets killed by operatives before she can explain. His father (Jason Isaacs) fights off one operative, but is killed as well, and Nathan runs away. He comes back to save Karen and defeats the armed operative, who tells him there's a bomb in the kitchen. Naturally, Nathan goes to look, and there's 7 seconds left! He and Karen run outside and leap into the pool as the house and operative are destroyed.
Karen is hurt, so Nathan takes her to the hospital. We see Mr. Kozlow arrive in country, and he gets undressed in a car. In the hospital, Nathan calls 911 about his parents murdered but the operator told him to hold the line and the call connects to Frank Burton (Alfred Molina) of CIA, who tells him to stay put, and Kozlow's goons apparently have the pay phone tapped! His shrink, Dr. Bennett, uses balloons to hide Nathan from the hospital cameras, which everyone has tapped into as well. In a car escaping, Dr. Bennett explains that she's with the CIA, and Burton can't be trusted. She tells him it's ok to trust Martin Price or Paul Rasmus, but doesn't explain why. She also gives him keys to a safe house in Virginia. They leap from the car and Dr. Bennett's car is destroyed. By this time, if you're not completely dazed, you realize Nathan is some kind of important kid, with secret skills.
Nathan and Karen wake up in the woods, completely refreshed and clean. Burton briefs a bunch of constipated agents about Martin Price, who is Nathan's real father, and has stolen data from Kozlow. Burton's boss tells him to get things under control. Nathan and Karen hitchhike to the safe house, where he finds a gun, a phone with encrypted text and some photos, who he recognizes as his mother. Karen makes a phone call, and apparently all of her relatives' phone lines are tapped too.
Nathan's father left a BMW, and Nathan/Karen go looking for his mother, finding her grave. They find fresh flowers on the grave, and the cemetary operator tells them the flowers came from Paul Rasmus. The bad guys and the CIA intercept the cemetary computer query, even though it's not on the internet, and magically conjure an image of the BMW, apparently from the cemetary's high-resolution cameras. Nathan and Karen meet Gilly, who gets them fake IDs. They buy train tickets, but the bad guys have spotted the BMW and followed them to the train station.
On the train, Karen asks if they are going to die, and Nathan says no. They kiss and start to grope, but stop because they're hungry? Karen goes to get food without him, and guess what happens next - the bad guys get her! Nathan, who has gone looking for Karen, meets the bad guy and they fight. Nathan manages to beat a grown, trained operative and Karen escapes her bondage with a piece of broken glass. Nathan shatters the train window and throws the bad guy out. The train stops, perhaps to investigate, and they exit the train. At this point, you're hoping the movie is over, but there's still 30 minutes left!
Natah and Karen stroll through the woods, and the CIA chases them. Burton convinces them to trust him and buys them burgers, while about 100 agents protect them. Burton explains things, and Kozlow's bad guys start killing the CIA guys. Nathan realizes the phone has the text his father stole, and that Burton's name is on in the text. The bad guys attack the diner. During the attack, Nathan and Karen escape, and since Nathan doesn't trust Burton he tells Karen about the list. Of course, Kozlow can hear them and track them, so he calls the phone in the car and threatens all of Nathan's friends and arranges a meet. Meanwhile, the CIA raids Kozlow's hideout and kills his goons. They also find a recording of the conversation between Nathan and Kozlow, detailing the meet at PNC park in Pittsburgh.
At the park, Martin calls Nathan and tells him not to go through with the meet. Nathan hangs up on him. Karen gets a photo of Kozlow and sends it to Nathan. They sit beside each other, and apparently, Gilly has taped a gun under Nathan's seat! Kozlow tells Nathan that his parents were awful people, and Nathan chooses to believe him. We relive Nathan's mother's death at the hands of Kozlow, and even at age 2, Nathan was a super-spy! Kozlow gets Nathan's gun, then chases him through the park. Nathan demonstrates his parkour abilities, and Martin calls him to tell him to lead Kozlow into a trap. Kozlow has time to see Martin hidden as a sniper about 500 yards away, and has time to yell before getting shot. Burton's boss arrives and take the phone, telling Burton he has lots to answer for. The CIA lets Nathan go, and Martin calls one last time to say goodbye. Karen and Nathan reunite, and Dr. Bennett arrives as well. She tells Nathan he can live with her, and Nathan/Karen stroll off, promising to go to Dr. Bennett's house (even though she never gave an address - apparently, Nathan can figure that out, too).
Nathan and Karen sit in the now-empty stadium and make out.