Eighteen months after the events of "Day 3", CTU is now headed by Erin Driscoll, a steely government agent who made firing Jack one of her first priorities upon taking over. After the explosion of a commuter train, Jack, who is now working for Secretary of Defense James Heller, while secretly romantically involved with Heller's married daughter Audrey, suddenly finds himself heading back to CTU for a meeting with Driscoll on Heller's behalf.
Chloe goes to Jack with the information from her college friend and he gets reinstated by Driscoll on a provisional basis for the pick-up. Behrooz is followed to a drop-off site by his girlfriend. Heller and Audrey are held captive by the terrorists.
Jack allows Andrew Paige to be taken hostage so that he can follow the terrorist back to Heller, endangering Andrew and alienating Chloe. Behrooz goes to his mother for help in keeping Debbie out of harm's way. Curtis steps up his interrogation of Richard Heller. Marianne Taylor joins the CTU team.
In an effort to stall one of the terrorists while a satellite is positioned to track him, Jack stages a gas station robbery. Heller and his daughter make a daring escape attempt. Driscoll learns of Chloe's involvement in Jack's activities. Debbie is poisoned by Behrooz's mother Dina. Jack runs into a police blockade while escaping his robbery.
After the police make a grave mistake with the handling of Kalil, Jack and Driscoll form an uneasy alliance. Audrey and Heller go to drastic measures in hopes of staving off the upcoming court trial. Meanwhile, Driscool tries to bargain with Chloe to eliminate her from the current situation, while problems for the Araz family begin to mount in their attempts at concealment.
Against the wishes of his superiors and with the knowledge that the terrorist base is about to be demolished with bombs, Jack goes in to rescue Heller and Audrey.
Jack and Audrey go to view the event recording where Audrey had seen one of the terrorists. When trapped, Jack makes a call for help from an unexpected ally, Tony. Sarah starts to suspect Marianne's misdeeds. Edgar attempts to shut down the nuclear cores from CTU and while it works on some, others remain under terrorist control. Dina tries to help her son escape his father, but takes a bullet in the process.
Jack informs Heller that someone at CTU leaked their location and set up an attack on Jack and Audrey as they looked for the man she recognized. Heller tries to reveal the spy by releasing false information on Jack's whereabouts and seeing who sends it out.
Behrooz steps out to get pain medication for his wounded mother even as Jack and his team sweep in to take her into custody. Edgar tries to get help for his mother who is in the path of fallout. Navi takes Behrooz hostage in the basement of the hospital and Dina makes a deal with Jack to help if he can save her son.
Jack rescues Behrooz from Navi, but Behrooz grabs a gun and kills his father. Dina gives Jack the only information she knows about the terrorist connections and he discovers a basement full of their plans.
Jack gets information from Paul Raines through electrocution, even as Audrey looks on. Tony gets Dina to reveal all she knows about the terrorist cells she worked for and the identity of Marwan through his threats of what will happen to Behrooz should he go to jail.
Jack and Paul try to gain information on Marwan at the company headquarters but the superiors, fearing repercussions, act against them. Erin steps down and Tony volunteers to fill in on a temporary basis. The company sets off an EMP to safeguard their secrets, enveloping downtown in darkness and leaving Jack and Paul stranded. Erin's permanent replacement arrives and it's Tony's ex-wife Michelle.
Michelle steps in as head of CTU even as Jack and Paul fight for their lives against mercenaries in the devestation of the EMP bomb. Michelle fires Gavin when Gavin asks Michelle to honor Driscoll's agreement. Jack and Paul hole up in a sporting goods store with its two owners who refuse to leave despite the danger. Paul takes a bullet meant for Jack.
Jack tries to get to Marwan by having Dina pretend to abduct him, but his plan is eventually sniffed out. The team following Jack is killed as is Dina. Marwan's agent infiltrates an Air Force base after disposing of a pilot and gaining his clearance. Chloe returns to CTU service.
CTU tries to find Jack's location after he's taken hostage by Marwan. Marwan stages a trade, Jack for Behrooz, in an effort to keep CTU's resources from discovering his real objective. This leads Curtis to an interrogation session with Behrooz, believing that Behrooz may know something. Mitch Anderson prepares for takeoff.
Jack and a team find the location where Marwan had kept Jack, but Marwan escapes. The files they discover reveal the identity of Mitch Anderson even as President Keeler heads towards Los Angeles to address the nation.
Air Force One crashes after receiving an indirect air-to-air missile hit. With the President missing, the Vice President is sworn in. Two campers stumble across the wreckage of Air Force One and the "nuclear football".
While Marwan secures a nuclear warhead, one of his lieutenants makes a mistake with a credit card and when Curtis arrives to take him and Joe Prado, the man meeting him, into custody, Prado kills the other man before surrendering.
After Jack's physical interrogation of Joe Prado the President sends the Secret Service out to arrest Jack. CTU agents try to trap Marwan at a club. The Secret Service show up at the club and arrest Jack.
David Palmer is brought in by Logan to head up the investigation into the missing warhead. Palmer issues a command to Jack to secure a lead, even if it means a secret attack on the Chinese Embassy.
The Chinese security director arrives at CTU to determine their involvement after the security camera tapes reveal a CTU agent. Palmer and Novick try to come up with a plausable cover-up story. Lee reveals a possible Marwan location and Jack takes him captive but not before the nuclear missile launches.
The Speaker of the House questions Logan's ability to lead so he stages a disagreement with Palmer. Audrey's brother Richard is once again brought in for questioning when his phone records reveal a call to Marwan.
Mandy contacts Michelle at CTU and asks for her help in exchange for Tony's life. Mandy then sets it up to look like the two of them die in an explosion, devestating Michelle.
Mandy tells Jack where to find Marwan and though they arrive in time to stop his helicopter from taking off, Jack can't keep Marwan from falling to his death.