Disbelieving, Jerry is caught by the FBI and interrogated by Supervising Agent Tom Morgan (Billy Bob Thornton). While Morgan is conferring with Air Force OSI Special Agent Zoe Pérez (Rosario Dawson), the woman on the phone arranges for Jerry's escape and directs him to Rachel Holloman (Michelle Monaghan), a single mother. The woman on the phone is coercing Rachel by threatening her son Sam (Cameron Boyce), who is en route to the Kennedy Center with his school band. The woman on the phone helps the two avoid the Chicago police and FBI, with the ability to control networked devices, including traffic lights, mobile phones, automated cranes, and even power lines.
Meanwhile, the woman on the phone redirects a powerful DOD crystalline explosive (hexamethylene) to a gemcutter who cuts and fits it to a necklace. Another man (Anthony Azizi) is manipulated into stealing Sam's trumpet from Chicago and fitting the crystal's sonic trigger into the tubing before forwarding it to Sam in Washington, D.C.
Agent Perez is summoned by Secretary of Defense George Callister (Michael Chiklis) to be read into Ethan's job at the Pentagon. Ethan monitored the DOD's top secret intelligence-gathering supercomputer, the Autonomous Reconnaissance Intelligence Integration Analyst (ARIIA; voiced by Julianne Moore). Callister leaves Perez with Major William Bowman (Anthony Mackie) and ARIIA to sort out the Ethan Shaw investigation. Simultaneously, Rachel and Jerry learn that their mysterious woman is actually ARIIA, and she has "activated" them under the Constitution's authorization to recruit civilians for the national defense.
Perez and Bowman find evidence Ethan Shaw hid in ARIIA's chamber the night he died. After they leave to brief Secretary Callister, ARIIA smuggles Jerry and Rachel into her observation theater under the Pentagon. Both groups learn that after her recommendation was ignored and a botched operation in Balochistan resulted in the deaths of American citizens, ARIIA concluded that "to prevent more bloodshed, the executive branch must be removed." Acting on behalf of "We the People", and citing the Declaration of Independence ("whenever any Form of Government becomes destructive of these ends, it is the Right of the People to alter or to abolish it"), ARIIA acted in compliance with Section 216 of the Patriot Act which "allows us to circumvent probable cause in the face of a national security threat, in this case, the chain of command itself."
Too late realized, Jerry has been brought by ARIIA to circumvent biometric locks his twin placed to prevent the system from realizing Operation Guillotine, a military simulation of how to keep the government running with the loss of all presidential successors. Because of Secretary Callister's concurrence with ARIIA's abort recommendation regarding Balochistan, he has been chosen as the designated survivor after the hexamethylene detonates at the State of the Union address (SOTU).
One of ARIIA's agents (Nick Searcy) extracts Rachel from the Pentagon and gives her a dress and the hexamethylene necklace to wear to the SOTU. Sam's school band has also been redirected to the United States Capitol to play for the president, bringing the trigger in Sam's trumpet and the explosive together. Jerry is recaptured by Agent Morgan, who has become convinced of Jerry's innocence. Though Morgan sacrifices himself to stop an armed MQ-9 Reaper sent by ARIIA, he first gives Jerry his weapon and ID with which to gain entrance to the Capitol. Arriving in the House Chamber, Jerry fires the handgun in the air to disrupt the concert before being shot and wounded by the Secret Service.
Days later, Secretary Callister reports that ARIIA has been decommissioned and that he recommends against building another; the Shaw twins, and Agents Perez and Morgan receive awards for their actions; and in the final scene, Jerry attends Sam's birthday party, earning thanks and a kiss from Rachel.