Eighteen months have elapsed since the conclusion of Day 3. A commuter train bound for Los Angeles explodes. A man steals a suitcase from a passenger in the wreckage and then kills him. Jack has been dismissed from CTU and now works for Secretary of Defense James Heller. Jack is involved with Heller's daughter, Audrey, and their relationship is growing serious. Jack is in LA for a meeting with CTU Director Erin Driscoll, who fired him a year ago, but he finds himself alienated at CTU by Driscoll and the new staff when reports of a possible terrorist strike come in. A young computer hacker named Andrew Paige sees something that he shouldn't on the Internet. Suddenly, he finds himself running for his life as he is pursued by terrorists. Luckily, he is able to warn Chloe O'Brian before its too late. The Turkish Araz family are not what they seem and it becomes clear that they are heavily involved with the day's events. Meanwhile, Heller has a confrontation with his estranged son. Jack finds that Chloe is his only ally as he tries to prove that the train explosion is merely a diversionary target.
Jack pushes Driscoll to reinstate him in the wake of Heller's kidnapping. He finds himself working as a subordinate when the Field Ops team goes to pick up Andrew. Behrooz finds himself torn between his loyalty to his parents and his feelings for his girlfriend as he is sent on his first assignment. Heller tries to comfort his daughter as his captors broadcast their intensions on the Internet.
Jack tracks Kalil with Chloe's aid, but is forced to watch helplessly as Andrew is tortured for information. Behrooz pleads with his parents when they order him to bring Debbie to their home for questioning. Curtis uses harsh methods to interrogate Heller's son as Driscoll continues to search for Jack.
Jack acts as a bandit and takes hostages to buy Chloe more time to get satellite surveillance. Meanwhile, Chloe must confide in Edgar for help when Driscoll becomes suspicious. Behrooz discovers just how far his mother is willing to go to insure that their secret mission is successful. Heller and Audrey attempt to escape from Omar, while Driscoll uses her influence to deal with a personal crisis.
Jack and Driscoll agree to work together when the police make a critical error in dealing with Kalil. Heller and Audrey take drastic action in the hopes of avoiding the impending trial. Driscoll makes a deal with Chloe to get her out of the way, while the Araz family faces another problem in their cover-up.
Jack initiates a fierce gun battle with the terrorists as he races to rescue Heller and Audrey before the military strike begins. Dina questions her own dedication to their cause when her husband reveals his plans for Behrooz. Driscoll and Curtis uncover new evidence that points to an even bigger attack by the terrorists. Audrey has an awkward meeting with her husband, and Heller butts heads once again with his son.
Jack takes Audrey to ID the man she recognized at the compound, but the terrorists get there soon after and pin them down. Jack must call on an old friend to help him escape. Heller puts Edgar in charge of dealing with the nuclear override, while Driscoll's daughter takes a turn for the worse. Dina is wounded when she helps Behrooz flee from Navi. Navi's boss orders him to hug his wife and son before the day is over.
Jack and Audrey hide out with an embittered Tony as Audrey makes a positive ID of the man from the kidnapping. Marianne successfully diverts suspicion from herself, leading Driscoll to torture the wrong person for information. Behrooz takes Dina to a hospital for medical attention, but the doctor becomes suspicious of her gunshot wound and phones the police.
Jack and Tony are able to trace Dina's location, but Behrooz slips through their fingers. Dina demands a full pardon for her son in exchange for information on the override device. Edgar wrestles with his emotions when his mother is trapped in the path of the nuclear fall-out. Behrooz turns to his uncle for help, but Navi closes in on him before he can get away.
Audrey places herself in a compromising position when she and Jack learn of her husband's possible involvement with the terrorists. Marianne offers Curtis information on the location of the override device in exchange for a lighter sentence, but the tables soon turn and Curtis discovers that there's another player in the game. Sarah bargains for a stronger position at CTU, while Tony takes charge of the interrogation of Dina and Behrooz.
Jack and Curtis finally learn the location of the override device. They try to trap the architect of the terrorist strike before the remaining nuclear plants go critical. Tony pushes Dina to reveal more of her knowledge of Marwan, while Driscoll faces another personal crisis with her daughter.
Jack and Paul visit the defense contractor who employed Marwan, but the company executives put their own interests ahead of CTU's and take major steps to destroy evidence. After a grief-stricken Driscoll relinquishes her command, Heller appoints Tony as interim director to oversee the latest crisis.
Jack and Paul are hunted down by soldiers after an electromagnetic pulse bomb wipes out every electrical device for miles. Meanwhile, Michelle Dessler takes over at CTU.
Jack learns the identity of a man who may be able to lead him to Marwan. He forces Dina to help him in a mock hostage situation that will get him close to the suspect. Michelle calls on Chloe for help when Edgar begins to crack under pressure. Meanwhile, Audrey stands by as a gravely wounded Paul is taken into surgery. Marwan's plan continues as his henchman uses an unwilling pilot to gain access to an airfield.
Marwan decides to trade Jack for Behrooz in hopes of distracting CTU from his real objective. Tony and Michelle weigh the consequences of the trade, while Curtis reluctantly interrogates Behrooz in order to learn more about Marwan.
CTU raids Marwan's hideout, but he manages to slip through their fingers. Luckily, Jack locates a lead that may help him identify Marwan's next target. Tony becomes suspicious of Michelle's personal life, while Audrey reunites with Paul and learns the extent of his injuries. Anderson closes in on his quarry, as President Keeler searches for words that will comfort the American public.
Mike pushes for the Vice-President to be sworn into office as the White House waits for news of Keeler's fate. Two innocent bystanders are dragged into the fight as Jack and Marwan both pursue a briefcase that contains the launch codes for America's nuclear arsenal.
Curtis brings in a suspect who has critical information about Marwan's next strike. Michelle orders Curtis to use harsh methods to interrogate the suspect, but things get complicated when Marwan sends a lawyer to defend his rights. Logan's advisors begin to worry as he continues to exhibit fear in the face of the ongoing terrorist threat.
Chloe is unexpectedly thrust into fieldwork when a woman reports that her boyfriend may be part of the terrorist conspiracy. Jack and Curtis find their latest efforts to trap Marwan thwarted by the Secret Service, who have orders to arrest Jack for insubordination. Mike calls on ex-President David Palmer for help as Logan continues to display a lack of leadership.
After Logan authorizes Palmer to take charge of the crisis, Palmer sanctions Jack and Curtis to infiltrate the Chinese Embassy on a covert operation to capture a suspect. Tony and Michelle continue to bump into each other's personal lives, while Buchanan expresses anger at being kept out of the mission. Jack faces Audrey's wrath when a medical dilemma places Paul's life in jeopardy.
CTU scrambles to forge an alibi when a Chinese representative produces evidence of American involvement in the raid on their embassy. Audrey gives Jack the cold shoulder, while Palmer and Logan clash over the consequences of Palmer's decisions. Jack and Curtis close in on Marwan as the countdown for the missile launch moves ahead.
Jack finds that his efforts to bargain with Marwan for the location of the missile strike are futile. Heller pushes his son for information when CTU discovers that he may have had contact with Marwan before the attacks. Logan finds himself in the middle of a power struggle between Palmer and the ambitious Speaker of the House. Tony and Michelle explore their rekindled passion for each other, but their hopes for the future may be short-lived when a familiar player enters the game and takes a hostage.
Mandy uses Tony as leverage to try to force Michelle to aid in her escape. A Chinese security operative captures and interrogates one of the CTU agents involved in the raid on the embassy. Palmer and Logan argue over the option of evacuating all major cities that may be targets for the missile.
As the missile speeds toward its destination, Mandy cuts a deal with Jack and the President to give up Marwan's location in exchange for a full pardon on all of her crimes. Tony and Michelle share a happy reunion, but Jack finds his relationship with Audrey shattered as she makes her feelings known. Logan's advisor suggests a drastic course of action when the Chinese government demands that Jack be handed over to them for trial. Palmer tries desperately to warn Jack of the danger against him. Jack's life changes forever as Tony, Michelle and Chloe help him to evade the trap set for him by Secret Service.