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. In L.A., David Palmer is visiting his brother Wayne, when he is killed by an assassin's bullet. As CTU scrambles to gather more information, an exploding car bomb kills Michelle and injures Tony. Chloe is also pursued by an unknown figure, but she eludes him and manages to contact Jack for help. President Charles Logan and his wife Martha are visiting L.A. and are planning to sign an important arms treaty with the president of Russia. Martha seems to be unstable and is badly shaken by the news of Palmer's murder. Logan refuses to heed CTU's warnings of possible danger and call off the summit. Jack is forced to take Derek along for the ride as he meets with Chloe and fights off a group of men who want him killed. He forces one of the men to confess that Jack has been deliberately framed for the murders of Palmer and Michelle.

Jack and Chloe infiltrate Wayne Palmer's penthouse where David Palmer was assassinated, in the hopes of finding a clue to his murder. 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. CTU and Secret Service attempt to capture Jack, but they only find Chloe as Jack and Derek slip through their grasp. Martha tries to convince her husband that she received an important phone call from Palmer the night before his death, but a tape of their conversation seems to contradict her claims. Jack goes to the airport to find a lead, but a group of renegade Russian terrorists take hostages, including Derek, before he can act.

Jack conceals himself inside the airport hanger and surveys the Russian separatists, feeding information to Curtis and his assault team. The terrorists begin executing hostages in an attempt to make Logan cave into their demands. Martha discovers that all traces of her conversation with Palmer may not have been erased.

Jack is captured by the terrorists, who use Derek as leverage to force him to compromise CTU's assault operation. Logan refuses to give into the terrorist demands as the time of the co-signing of the treaty draws near. Martha tries to tell her husband of the evidence she uncovered about her phone call with Palmer, but Walt interferes with her efforts. A new representative from District arrives at CTU and begins to undermine Buchanan's authority.

Jack returns to CTU and has an emotional reunion with Audrey, while Curtis tracks the Russians and the stolen nerve gas. Walt sends in a hit man to silence Jack. Chloe discovers that Spencer has his own agenda at CTU. Walt convinces Logan to have Martha institutionalized when she tells them of the attack on her.

Jack contacts Mike and asks for a secret meeting in hopes of gathering evidence against Walt. Martha begs Aaron for help, while a desperate Walt tries to force Logan to aid him in his complicity with the terrorists. Buchanan butts heads with Lynn over a decision to violate the president's orders, while the Russians attempt to escape with the nerve gas.

Jack tracks down a man who has a connection to the terrorists. Logan is forced to grant him immunity in exchange for information on their whereabouts. Mike and Martha argue over Logan's public response to Walt's involvement with the Russians. Lynn is drawn away from his post by a personal crisis as the terrorists come closer to striking against the U.S.

Jack poses as Rossler and manages to trace one of the canisters of nerve gas, but he goes against orders from the president when the terrorists target a shopping mall. Logan and Martha quarrel when she learns of her husband's intention to cover up the real reason for Walt's suicide.

Lynn orders Curtis to take Jack into custody for violating presidential orders, but Jack breaks away from Curtis when Nathanson contacts him through Audrey and offers information on the location of the nerve gas. Lynn begins to unleash on his coworkers as he discovers that they may be working against him to aid Jack. The head of the terrorists makes a demand on Logan, and Martha takes a dangerous step to get her husband's attention.

Logan wrestles with his conscience when he learns that Martha is riding in the motorcade with the Suvarovs. Audrey convinces Curtis to take action as Lynn continues to abuse his authority. Jack learns that an ex CTU agent, Christopher Henderson, works for a company which is connected with the nerve gas.

Jack interrogates Henderson's wife about her husband's connection to the terrorists. Lynn begs his sister to return his stolen keycard, while Tony regains consciousness and learns of Michelle's fate. Martha gives Logan the cold shoulder, while Curtis tracks another nerve gas attack to a local hospital.

Jack takes Henderson to CTU for questioning. Once there, he faces an unhappy reunion with his daughter, Kim. Mike appeals to Martha for help as Logan faces pressure from his Vice-President to declare martial law on L.A. Lynn connects the theft of his keycard to an impending strike on CTU, but his warning comes too late to stop a terrorist from infiltrating the building.

Jack and Lynn must take action when they discover that the nerve gas is breaking through the protective seals that are keeping the CTU survivors alive. Chloe wrestles with her grief over Edgar's death, while Tony contemplates revenge against Henderson. Martha bolster's Logan's spirit as he wavers under more political pressure from Gardner.

Jack bargains with a German intelligence agent in order to find the woman who can lead him to Bierko. Buchanan chafes against the new chain of command as Homeland Security prepares to take over CTU operations. Aaron receives a request for a secret meeting from Wayne Palmer, as Logan implements martial law in L.A.

Jack pushes Audrey for answers when evidence indicates that she may be involved with the terrorists. Wayne and Aaron flee from a group of gunmen who have orders from Henderson to kill them. Bierko and his men gain access to a natural gas plant, where they plan to distribute the nerve gas throughout L.A.

Jack and Wayne locate a source inside Logan's administration who has information on Palmer's assassination. But things get complicated when they learn that Henderson is using leverage to keep her silent. Audrey is forced to choose between Chloe and Buchanan as Homeland Security begins to absorb CTU.

Jack and Wayne locate a recording that definitively proves Logan's involvement in the terrorist conspiracy, but Henderson corners them in the hopes of destroying the incriminating tape. Logan tries to cover his tracks by issuing a warrant for Jack's arrest. Audrey contacts her father for help, while Chloe gives her cover while helping Jack evade CTU.

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.

After stowing away aboard the flight containing Henderson's contact and the incriminating recording, Jack finds himself having to deal with a pilot who refuses to cooperate. Martha begins to break down, and Mike becomes suspicious of what she is hiding from him, while Logan tries to calm his financial backers.

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.

Bierko escapes from the transport taking him to Division and uses his last canister of nerve gas for a surprise strike. Jack is forced to work with Henderson to find Bierko, but Henderson wants something in return. Logan takes drastic steps to deal with Aaron when he won't go along with the cover-up.

Jack and Henderson wage an assault on the submarine as Bierko prepares to launch an attack against L.A. Chloe brings in someone from her past to aid her. Martha and Aaron enlist Mike's help in their plans to expose Logan.

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.