18 months have passed since the events of Day 4. With the exception of David Palmer, Tony Almeida, Michelle Dessler and Chloe O'Brian, the world believes that Jack Bauer is dead. Jack is living near L.A. under the name of Frank Flynn, working on an oil rig and living with Diane Huxley and her teenage son, Derek.
Jack and Chloe infiltrate Wayne Palmer's penthouse where David Palmer was assassinated, in the hopes of finding a clue to his hug. Jack convinces Wayne to cooperate and finds some information in Palmer's memoirs that leads him to the airport where the Russian president is about to land.
Jack works with CTU from his hidden position within the airport terminal whilst Curtis prepares an assault plan.
Martha Logan attempts to track down a hard copy of her phone conversation with David Palmer.
Having forced Jack out of hiding, Beresch sets a trap for Curtis and his men. President Logan worries over the possibility of more innocent lives lost as the treaty signing approaches.
Lynn McGill arrives from District to oversee things at CTU.
CTU is forced to investigate its own staff while a touching reunion between Jack and Audrey turns awkward. As the national threat worsens, unexpected players and ulterior motives surface and President Logan begins to break down.
In order to locate the nerve gas quickly, Jack enlists the help of Mike Novick to get to Walt Cummings.
Meanwhile, Martha accepts defeat when she's found in the stables and prepares to be admitted into a psychiatric clinic.
Ivan Erwich begins the process of reconfiguring the triggering mechanisms on the nerve gas canisters with the aid of Jacob Rossler. Martha persuades her husband to go public about his Chief of Staff and they work together on a statement for the press.
Jack and Curtis infiltrate Rossler's building which leads to a difficult situation for Jack. Meanwhile, Lynn is pulled away from CTU by his troublesome sister.
Jack goes undercover as Rossler and delivers the chip for the remote trigger to Irwich's men in the hopes that they will lead CTU back to Irwich and the nerve gas canisters. However, all does not go to plan and Jack is forced to help the men release a canister of nerve gas in a public place.
Martha comforts Walt Cummings' widow, Suzanne, as she arrives to pick up her late husband's body.
Jack gets another lead when Nathanson decides to contact him. A new face emerges amongst the Russian terrorists and President Logan is forced to make a difficult decision. Lynn is on meltdown as the pressure on him increases.
President Logan learns of his wife's whereabouts and desperately tries to persuade her to leave the motorcade before the imminent attack by the Russian terrorists. Audrey, Chloe and Edgar work behind Lynn's back as they help Jack follow up on a lead which reunites him with the man that brought him to CTU. Wanting to avoid further embarrassment, Lynn stops listening to his colleagues and the situation comes to a head at CTU.
Tony regains consciousness and wonders how Michelle is doing. Martha and the Suvarovs head back to the retreat where Yuri makes known his observations of Martha's erratic behaviour to President Logan. Lynn tries to persuade his sister to give the keycard back. CTU find a schematic on one of the dead terrorists and attempt to locate their next target. Meanwhile, Jack heads to Christopher Henderson's house and questions his wife.
Vice President Hal Gardner joins the President to offer new suggestions on how to deal with the terrorist threat to the dismay of Mike. CTU is infiltrated by Bierko's man using Lynn's keycard. Tony wants to know who's responsible for Michelle's death. Christopher Henderson is taken back to CTU and interrogated.
The remaining CTU personnel discover they don't have much time in the safe zones. They will have to take matters into their own hands if they're to survive. Hal Gardner's influence over President Logan increases but Mike and Martha intend to put a stop to it. Homeland Security makes plans to take over CTU and Tony holds back from exacting his revenge on Henderson for Michelle's death but for how long?.
President Logan declares martial law in Los Angeles despite his wife's apprehension. Homeland Security begin their assessment of CTU prior to their intended takeover. Wayne Palmer arranges to meet with Aaron Pierce in order to give him something. Vladimir Bierko plans to hug 200,000 people with his next attack whilst Jack and Curtis track down Collette Stenger.
Vladimir Bierko launches his final attack which could possibly be his most lethal. Shari Rothenberg arrives to replace Edgar but Miles is not too happy to see her. Jack interrogates an unlikely suspect and an assault team is sent out to stop the deployment of the remaining nerve gas but are they too late?.
Karen Hayes is finally forced to realign CTU by Vice President Gardner but Bill isn't going to step down easily. Miles puts forward a plan to use Audrey and her split loyalty between CTU and DoD in an effort to justify the takeover. Wayne Palmer reveals the identity of his brother's source in the White House and Jack goes after Henderson. Suspicion mounts on the Vice President as the mastermind behind the day's events.
Jack and Wayne leave Evelyn and her daughter in a motel room whilst they recover the recording they need from a bank vault. Audrey arranges a meeting with her father so that a credible figure in the government can present the evidence once it's been retrieved. President Logan orders Karen Hayes to issue a warrant for Jack's arrest.
Jack shows Heller the incriminating recording in the hopes that he will help them take down Logan, but Heller has plans of his own that will save face for the presidency. Miles tricks Chloe into leading CTU to Jack and Audrey. Mike and Martha both become more suspicious of Logan's actions, while Heller confronts the president with an ultimatum.
Jack captures Henderson and attempts to force him to hand over the recording, but Henderson targets Heller to buy himself more time. Logan confesses his involvement in Palmer's assassination to a distraught Martha. Miles traces Chloe to Buchanan's home, but Hayes finds herself questioning Logan's motives as CTU closes in.
Having been warned by Karen Hayes, Chloe manages to escape the Homeland Security team sent to capture her. Jack searches for the recording on the flight whilst Martha is having trouble coming to terms with her husband's involvement in the day's events. President Logan faces mounting pressure from Graham to find Jack, Mike suspects there's more to Martha's behaviour than she's letting on and Jack has the plane's captain to contend with.
Jack searches for a safe place to land the plane when Logan gives orders to shoot it down. Hayes readies Bierko for a transfer to a secure facility, while Audrey receives some good news about her father. Logan becomes desperate as his plans start to unravel, but an unexpected ally at CTU turns the tables in his favor.
Moments away from a video conference with the Attorney General to present the evidence against President Logan, Jack, Chloe, Bill and Karen discover that the recording has been wiped. CTU are informed of Bierko's escape and Jack is forced to work with an old foe in order to work out where Bierko will target next. Martha stumbles upon Agent Adams in the midst of doing her husband's dirty work.
Jack and his team must find a way to board the submarine that Vladimir Bierko has locked down and prevent its missiles from being launched. A glimmer of hope arises in the form of a lone survivor inside. Martha brings Mike into the fold and Chloe has to enlist the help of her ex-husband.
Jack takes his fight directly to the President as he attempts to force a confession from him that will prove his involvement in the day's events. Martha vents her hatred for her husband in front of the press as Logan gives a eulogy over Palmer's body. Jack and Audrey share a tender moment when it seems the crisis has subsided, but Jack finds that his problems have only begun as his past catches up with him.