The United States armed forces have a lead on a suspected terrorist in Baluchistan, Pakistan. They plan to take him out during a funeral ceremony, but as the man has been a recluse, getting a positive ID proves difficult. The Department of Defense's new computer system recommends that the mission be aborted due to the uncertainty. Defense Secretary Callister (Michael Chiklis
) agrees with the abort recommendation, but the president orders the mission be carried out anyway. The result is a political backlash when all of the victims of the attack turn out to be civilians. Retaliatory suicide bombings across the world target US citizens in response.
Jerry Shaw (Shia LaBeouf
) is a Stanford University dropout who lacks direction and faces financial difficulty. He finds out that his more ambitious twin brother Ethan, an Air Force lieutenant with expertise in parallel algorithms and quantum electronics, has died, following a truck accident. Jerry had last seen Ethan three Christmases prior.
Following Ethan's funeral, Jerry goes to withdraw some money from an ATM and is surprised to see that he suddenly has $750,000 in his account. Money comes flying out of the machine and he scoops up most of it and takes off. When he returns home, he finds his apartment filled with a large number of weapons, explosives, and forged documents. He receives a phone call from an unknown woman who explains that the FBI is coming and will apprehend him in thirty seconds if he doesn't leave right then.
Not believing her, Jerry is caught by the FBI and sent to an interrogation room where he meets Special Agent Thomas Morgan (Billy Bob Thornton
). After some initial discussion, Morgan leaves the room to meet with Air Force Office of Special Investigations Special Agent Zoe Perez (Rosario Dawson
). She wants to interrogate Jerry. Morgan says no. While they are talking, a fax comes in from the Attorney General ordering the FBI to authorize one phone call to Jerry, after he'd already been told he would get no phone calls. An agent takes Jerry to a room with a phone.
Jerry picks up the phone and the unknown woman's voice comes on again, this time telling Jerry to get down flat on the floor. Within seconds, the wall caves in and a crane boom comes smashing through. Jerry sees an electronic sign on a building across the street, scrolling words that tell him to climb out and jump. He has now learned that the woman's voice and messages should be given serious attention, so he jumps and falls onto a subway track. The sign tells him to board the train. He does.
A cell phone sitting on top of a bag near Jerry rings and a message on the screen is for Jerry. He picks up the phone and answers it. It's the woman giving him further instructions. He's told to stay on the train, but he decides to try and escape by jumping over to another train. That train comes to a sudden stop and Jerry is called and told by the woman to listen and do what he's told. He's told to approach a car being driven by a single mother Rachel Holloman (Michelle Monaghan
). The "voice" has also been coercing Rachel into doing things by threatening to kill her son, Sam, a trumpet player on his way to Washington, D.C., from Chicago for a band recital at the Kennedy Center. When the woman spoke to Rachel, she told Rachel that she was "being activated."
When Jerry jumps into Rachel's car, she freaks out and fights and argues with him until he mentions her name and is able to calm her down enough to tell her what's been happening to him. The voice then comes across the GPS unit in the car and tells Rachel to get going. At the same moment, the police and FBI are on the scene and start shooting at them, so Rachel takes off. Multiple police and unmarked vehicles are after them.
The voice tells Rachel exactly how to drive, how fast, when to brake, where to turn, etc. The voice helps the pair to avoid the Chicago Police and FBI units, demonstrating the ability to remotely control virtually any networked device, such as traffic lights, cell phones, automated cranes, and even electrical wires. All of their pursuers are caused to be diverted or crash as Rachel and Jerry are directed into a wrecking yard. The large cranes in the yard are being remotely controlled and they eliminate the remaining police and FBI vehicles before grabbing Rachel's car and lifting it high in the air. Jerry and Rachel are told to stay in the car, but they decide to jump out anyway. They land on top of some garbage bags in a large barge that is cruising along in the nearby water. Rachel's car is dropped into the water.
At a military briefing at the Aberdeen Proving Grounds in Maryland, an officer is explaining the military's latest weapon as something with 80 times more explosive power than C-4. This new explosive is in the form of a hexagonal crystal and it's triggered by broadcasting a particular sonic frequency. 200 units of the crystal explosive are about to be sent out to field units. The voice has arranged for one of the crystals to be sent to a jeweler and the sonic device to be sent to a music store owner. Both men are unwilling participants.
The jeweler is ordered to create a necklace from the crystal, while the music store owner is ordered to insert the sound-based trigger inside Sam's trumpet. Sam is an unwitting participant in whatever is being planned.
Jerry and Rachel are directed by the voice to travel from Chicago to Washington, D.C. via Kendall County, Indianapolis and Dayton, Ohio. They start out on foot and as they are walking between two major power lines out in the country, a white van approaches and a man named Ranim Khalid (Anthony Azizi
) jumps out, thrusts a piece of paper at Jerry and throws the van keys onto the ground, saying "I'm done!" and he turns and runs away. The power lines then start arcing and fall to the ground, electrocuting Kahlid and cooking his body. Morgan and his men find a crystal on the body. It was Kahlid who'd produced the necklace from the larger crystal.
As they drive in the van to their next destination, Jerry and Rachel start arguing about his brother and her son and Jerry gets so upset, he pulls the van over, tosses the cell phone on the hood and begins walking away. Rachel chases after him, reminding him that they can't just walk away. The voice had warned them about the serious consequences associated with doing that.
Secretary Callister approaches Agent Perez and tells her it's time to bring her fully into the investigation she's involved with. He introduces her to a Major Bowman (Anthony Mackie
) and informs her that they suspect a terror attack of some sort is imminent. That information is based on their new massive computer system that monitors virtually every electronic-based system in the country and filters and consolidates information so that threats can be identified. The system is still in beta testing.
The computer system, referred to as the "Autonomous Reconnaissance Intelligence Integration Analyst" (ARIIA), consists of what appears to be hundreds of gold colored orbs situated along the walls of a large globe-shaped room. Another orb, attached to a movable arm, interacts with those attached to the walls. The voice of the computer system (voiced by Julianne Moore
) is the same voice that had been directing Jerry and Rachel. Secretary Callister orders ARIIA to assist Perez in her investigation.
As ARIIA directs Jerry and Rachel to a mall to obtain a change of clothes, Jerry tires of answering ringing cell phones and land lines and tells the ARIIA that he's not taking any more orders via phone. ARIIA tells him to proceed to the video room of a nearby Circuit City store. Over several television screens ARIIA introduces herself to Jerry and Rachel by flashing up photos and videos of everything they've ever done and been recorded via electronic media, including that of their families.
In light of the mistake made by the President in the botched terrorist assassination attempt, ARIIA has decided that the executive branch of the U.S. government is a threat to the public good and must be eliminated. ARIIA plans to destroy the President and his cabinet via something referred to as "Operation Guillotine." ARIIA has decided to leave Secretary Callister -- who has agreed with her recommendation to abort the mission -- as the successor to the presidency. ARIIA has not revealed any of this information to Jerry, Rachel, or even Secretary Callister, merely explaining that she is trying to help the people of the United States and Jerry and Rachel are being recruited for purposes of national defense.
ARIIA directs Jerry and Rachel to a side street where there's an armored car awaiting delivery of a package. They are directed to intercept the package. To do so, they have to grab a couple of sawn off shotguns and get the drop on two security guards. They are able to get away with the stainless steel briefcase the guards were carrying and ARIIA assists in the getaway by setting off alarms and fire sprinkling systems, causing people to spill into the street and enveloping Rachel and Jerry as they run from the pursuing armored car guards and police. ARIIA opens a locked gate so Jerry and Rachel can get out of the crowd and she eventually directs them to a Japanese tour bus that stops and picks them up.
Morgan, realizing that everything connected to a network of some sort was being monitored and controlled, approaches a small business near where Jerry was last seen. Viewing the old fashioned camera/VCR recording, he sees Jerry and Rachel boarding the Japanese tour bus. When he learns the bus is headed for the airport, that's where he and his men go.
During the bus ride, Jerry tells Rachel that his brother Ethan was always able to do things Jerry couldn't and he was always trying to help Jerry learn how to do things better so he'd look good in his father's eyes. Jerry figures that whatever Ethan was involved with, it now is incumbent on him to try and complete. He wants to do that for Ethan.
The bus drops them at the airport where a man walks up and hands Jerry an envelope containing a credit card and passports and he gives them their next instructions. Morgan and his men arrive at the airport and begin looking for Jerry and Rachel. As Jerry goes through security and places the briefcase on the scanner, ARIIA changes the view picture so it won't reveal what's inside. About that time, Morgan spots Jerry, draws his gun and gives chase. They run through the concourse, eventually exiting an emergency door and going into the luggage handling area, where Morgan fires at them, eventually catching up to them and engaging in hand-to-hand battle as they travel along on a moving belt. Morgan drops his gun and Jerry picks it up and points it at Morgan, but he doesn't shoot. Instead, ARIIA diverts Morgan along another belt that takes him to a holding area.
Jerry and Rachel are directed by ARIIA to an Air Force transport plane where the electronic lock on the briefcase is released, revealing two pistol shaped injection syringes. They are directed to inject themselves with a serum that will reduce their bodies' need for oxygen. Then they crawl into a storage container. Before they fall asleep, Jerry gets Rachel to talk about her son so that her mind will relax. He learns that her ex-husband was a disappointment to her and after she fell asleep, he whispers that he won't disappoint her.
At the Pentagon, where ARIIA is housed, Agent Perez discovers that Jerry's late brother, Ethan, worked as a technician on ARIAA and when he learned of her plan to destroy the executive branch, he used biometrics to lock it down. ARIIA needs to scan Jerry so that his biometrics can be used to unlock the system.
Perez and Major Bowman are viewing a video log of Ethan's last day on the job, working with ARIIA. Ethan strangely walks several times around the room and Perez finally notices he's holding a cell phone and it's flashing. She thinks it may be Morse code. Bowman interprets it to say "Fire Extinguisher." ARIIA picks up on their conversation and is ordering the video log destroyed. Bowman argues with ARIIA, but the computer deletes the log. Perez goes to a nearby fire extinguisher box and finds a memory card for a cell phone tucked in there.
After viewing the memory card, Perez calls Morgan and tells him that Ethan worked on a project called Eagle Eye for the Secretary of Defense and was trying to stop the project. He was subsequently killed when a large truck broadsided his car at an intersection. She tells him that the computer system, ARIIA, was attempting to carry out a plan to eliminate the President and other members of the executive branch of the government.
Perez and Major Bowman go to Secretary Callister and they take him to a sealed room to discuss what they've learned. The sealed room is to prevent ARIIA from hearing or otherwise learning the content of their conversation. Callister admits to them that the administration had relied on some false intelligence in targeting a terrorist leader and ARIIA had tried unsuccessfully to stop them.
Jerry and Rachel are delivered to the Pentagon and are taken 36 stories below ground, to where ARIIA is located. ARIIA orders Rachel to step away from Jerry, then it proceeds to do a biometric scan of his body, and gets him to read a few words put up on a screen. The result is a release of the lock placed by Ethan on Operation Guillotine. ARIIA shows Jerry CCTV footage displaying Ethan's fatal car crash, explaining that she orchestrated his death because he was a threat to her plans. Jerry and Rachel watch as the details of the plan flash across the monitors and the president and his cabinet are shown to be targets.
Jerry immediately regrets what he has done and is visibly agitated. ARIIA then instructs Rachel to eliminate Jerry to prevent him from re-establishing the lock on the program. Rachel points a pistol at Jerry, but she cannot bring herself to pull the trigger. Jerry even takes hold of the barrel of the pistol and holds it flush against his face, encouraging Rachel to pull the trigger and save her son's life. Rachel can't and Jerry chooses not to pull the trigger himself.
Rachel is escorted away by a man just before Morgan and other men come barging into the control room and arrest Jerry. ARIIA tells Rachel that she has one task remaining and that Jerry will be eliminated by other means.
ARIIA allows Major Bowman and Perez to exit the room they'd been meeting with Secretary Callister in, but slams the door shut before the Secretary can leave. She then creates a huge electrical disturbance and fire in the area outside the room, attempting to kill Bowman and Perez. They escape to an area under the floor. ARIIA explains to Secretary Callister what she's doing in terms of Operation Guillotine and how it was decided he will be the new president once the current president and his cabinet are exterminated. Callister is shocked and dismayed.
Having been warned by Agent Perez, Morgan believes Jerry's story and asserts his authority to get Jerry released to his custody. He then drives Jerry towards the United States Capitol, instructing him to dispose of any electronics he may have along the way.
ARIIA sends a MQ-9 Reaper UCAV after them. After the drone's first pass, their car is flipped and destroyed and they are able to get out and commandeer another vehicle. The drone attacks again while they are driving through a tunnel. Agent Morgan is injured such that he can't continue much longer. He gives Jerry his badge and gun and tells him to get to the capitol and search out the sergeant-at-arms and relay the code for a threat to the president so that the sergeant-at-arms will assist him. As Jerry takes off, the drone returns and sights in on him. Agent Morgan jumps into another vehicle and accelerates towards the approaching drone. He slams his vehicle into what looks like a large steel structure lying in the road. The steel structure is leveraged vertically and slams into the drone, destroying it.
Rachel is taken by her male escort to an office where he produces a new identification card for her and hands her a dress to put on. He also gives her the necklace containing the hex crystal. Rachel tries to persuade the man to work with her so they can help each other, but he won't risk the lives of his own family and tells her she has only a few minutes to get to the house chamber where the president will be delivering his State of the Union address.
Major Bowman and Agent Perez have made their way back to ARIIA and are attempting to destroy the computer by draining out the liquid nitrogen that surrounds the equipment to keep it cool. ARIIA interrupts their efforts by creating an electrical discharge that knocks them both into a pool of water located at the bottom of the chamber.
Rachel is greeted by a young female as she approaches the house chamber and is escorted to her seat in the balcony. The president's cabinet is announced and the members begin to file in. The president arrives. Sam's class, whose recital has been moved from the Kennedy Center to the capitol to play the national anthem prior to the president's speech, begins to play. The trigger that will set off the explosive necklace is set to activate when Sam plays a sustained "high F" on his trumpet corresponding to the word "free" in the last stanza of the national anthem. ARIIA had arranged this as poetic justice, believing the president to not be brave.
Jerry overpowers a guard standing at a barred gate that provides underground access to the house chamber. He puts on the guards uniform and manages to gain entry to the chamber just as Rachel is attempting to get to her son, but she is prevented from doing so by security. Observing the extreme fear and agitation on part of Rachel, Jerry jumps up onto a desk, draws his pistol and fires several shots into the air. The performance immediately stops as people scream and scramble for cover. Security rush the kids in the orchestra from the room. A confused Secret Service agent shoots Jerry 2-3 times, taking him down.
Back at ARIIA, Bowman unsuccessfully attempts to destroy the central orb of the computer as he is knocked back and down. Rachel then picks up what appears to be a pry bar and jams it into the orb, creating a massive short-circuit which takes ARIIA out.
In a committee hearing after the chaos ARIIA caused, the Secretary of Defense urges that another supercomputer like ARIIA should not be built: "sometimes the very measures we put into place to safeguard our liberty become threats to liberty itself," he cautions them.
Ethan posthumously receives the Medal of Honor and Agent Morgan posthumously receives the Commendation Medal, while Jerry, injured but alive and well, receives the Congressional Gold Medal.
The film ends with Jerry attending Sam's birthday party. He brings a big present (something Sam's father never did) and Rachel thanks him for attending, then tenderly kisses him on the cheek. She tells Jerry that she's glad he's there. He softly responds, "me too".