Jack creates a faux-hostage crisis in a convenience store trapping Kalil and several innocent bystanders to buy Chloe more time to get the surveillance satellite working properly. Dina murders Behrooz's girlfriend after she becomes suspicious. Audrey and Secretary Heller try to escape.
Jack and Director Driscoll agree to a truce and work together after the police make a mistake in handling the Kalil situation, which means that Jack also has to find a new lead. The terrorists begin to threaten Audrey unless Heller confesses to "war crimes" on camera in an hour.
Jack initiates a fierce gun battle with the terrorists as he races to rescue Audrey and Secretary Heller before the military strike. Dina is shocked to learn that Navi and Marwan plan to have Behrooz killed. Secretary Heller learns his son is a suspect and allows the interrogation to continue. Curtis Manning learns that the briefcase stolen from the train bombing contains a Dobson Override that could potentially give terrorists control of America's 104 nuclear plants.
Jack takes Audrey into the field in order to ID a suspect she recognizes from the compound, but the terrorists learn where they are and pin them down. Jack calls on an old friend to escape. Dina tries to get to Behrooz before Navi does. Edgar Stiles works overtime to get back control of 87 to 98 nuclear plants by taking their systems off-line before the Override gets to them.
Jack and Audrey hide out with Tony Almeida after escaping from the terrorists and learn the man they are looking for is an employee for McClennan-Forrester. Behrooz takes Dina to the hospital to get medical attention. President Keeler orders six cities to be evacuated. Secretary Heller tries to flush out the mole in CTU, but the evidence points in the wrong direction.
Jack and Tony stumble on to Dina and Behrooz's trail after a key suspect has been assassinated. Edgar tries all he can to get his mother out of the fallout zone of the San Gabriel Island nuclear power station. Driscoll and Curtis cover their tracks following the revelation about Marianne. Navi closes in on Behrooz when he tries to get medication for Dina.
Jack races to save Behrooz from his father when the situation turns into a hostage crisis. Dina points Jack and Tony to a safe-house where they find evidence that points to Paul Raines' involvement with the terrorists. Marianne leads Curtis to a computer that contains info on the terrorists, but Curtis feels like it could be a trap.
After finding out that Audrey's husband, Paul Raines, may have information about the override, Jack decides it's time for some "shock treatment". The lead that Curtis was following up on at the Rockland Building proves to be vital, just as the remaining 5 nuclear reactors prepare to meltdown. Meanwhile, Tony does some interrogating of his own, and Driscoll deals with devastating news.
Jack and Paul Raines visit the corporate headquarters of McLennan-Forster, the defense contractor that employed Marwan. The company executives activate an EMP bomb to destroy incriminating evidence in order to protect themselves. Tony is given temporary command of CTU after Driscoll resigns following her daughter's suicide.
Jack and Paul enlist civilian help when they must fend off mercenaries from McLennan-Forster. Tony discovers that Michelle is taking over command of CTU. Marwan orders an underling to kill an Air Force pilot and his family and assume the pilot's identity.
Jack and Dina's attempt to infiltrate one of Marwan's terrorist cells backfires on them. Michelle orders Chloe back to work when Edgar begins to crack due to emotional pressure. Paul is taken into surgery after getting shot. Anderson gains access to an airfield and gets closer to the stealth bomber.
In order to buy more time for Anderson to close in on Air Force One, Marwan calls CTU and tells Michelle that he is willing to trade Jack for Behrooz. Bill Buchanan arrives at CTU and assumes command. Curtis interrogates Behrooz for more information on Marwan.
CTU raids Marwan's headquarters, but somehow allow Marwan to slip through their fingers in the confusion. Jack learns that the trade-off was nothing more than another ruse. Jack tries to talk Anderson out of the mission, but it is too little, too late as far as Anderson is concerned.
Jack's only hope of keeping the President's nuclear football (a computer containing the codes of America's nuclear facilities) out of Marwan's hands lies in two innocent campers who witnessed the crash of Air Force One. Meanwhile, Mike Novick wants to immediately have Presidential authority shifted over to Vice President Charles Logan.
Jack discovers that Marwan's new objective is to find and activate a nuclear warhead after he realizes pages from "the football" are missing. Logan's presidency is not off to a good start when he starts showing signs of fear. CTU sends Curtis to intercept one of Marwan's subordinates, but a lawyer from Amnesty Global stalls the interrogation.
Chloe is sent into the field for the first time to look into the report of a woman who claims her boyfriend is part of the conspiracy. Mike Novick calls in Former President David Palmer to assist President Logan. Jack's methods are questioned.
Palmer authorizes an extraction mission on the Chinese Embassy in L.A, to be led by Jack and Curtis. The intended target is injured during the raid, and the Chinese Consul is shot in friendly fire by his own people. Jack forces the doctors to stop working on Paul and help the suspect.
Jack fails to stop Marwan from launching the nuclear warhead. Richard Heller becomes a suspect again and James Heller leads the interrogation. Mandy takes Tony hostage after he checks up on Richard's information.
The Chinese representative kidnaps CTU Agent Howard Bern in an attempt to learn who led the raid on the embassy. Palmer and Logan may have to evacuate major U.S. cities in the hopes of preventing nuclear disaster, and Michelle tries to save Tony.
Jack must hunt down Habib Marwan and stop the nuclear bomb that is nearing its target which is Los Angeles. The Chinese demand Jack after Bern's confession and President Logan makes a hasty decision on how to handle the situation.