Over a year has passed since the events of Day One. President David Palmer is fishing with his son in Oregon when he learns of an emergency. He is taken to his underground bunker, where he learns that a Middle Eastern terrorist group known as Second Wave is planning to set off a nuclear bomb in Los Angeles sometime that day. At CTU, George Mason is ordered to contact Jack Bauer, who may be able to provide a lead to the terrorists. Jack has been out of commission since the death of his wife. He is also estranged from his daughter Kim, who is now working as an au pair. He isn't interested in returning to work, but changes his mind when Palmer personally requests his help. Kim overhears her boss abusing his wife, so she locks herself and their little girl in the bedroom. Gary forces his way in and attacks Megan. A young girl named Marie is marrying a man who may have connections to the leader of the terrorist group. At CTU, Jack learns that the key to finding the bomb rests with a group of American terrorists whom he infiltrated once before.

Jack works to establish his cover with a small group of domestic terrorists. He learns that their target hits very close to home. Kim takes Megan and runs from the house, but Gary pursues them. Palmer and Eric disagree over how to deal with the media during the nuclear threat.

Jack warns Lynne about the impending bombing of CTU, but her efforts to alert Palmer are sabotaged by Eric, who has his own agenda. George locates the warehouse where the nuclear bomb was built, but his discovery results in an unexpected tragedy. Kim takes Megan to CTU, believing that it is the safest place for both of them.

George returns to CTU where he orders the medics to revive a badly injured Paula, who has vital information. Palmer comes down hard on Eric for his deception. Kim takes Megan to the hospital, but the staff accuses her of abuse. Jack locates the leader of the American terrorist cell. He learns that the woman who gave them inside information on CTU is an old enemy.

George refuses to allow Jack to assist in Nina's interrogation. Jack resorts to blackmail to change George's mind. Palmer and Stanton meet with a Middle Eastern ambassador who may be in league with Second Wave. Tony visits the Warner home and questions Reza about his possible connection with Syed Ali.

Jack begins his interrogation of Nina and pushes all boundaries in order to force her to divulge the name of her contact. Palmer is surprised and suspicious when his ex wife Sherry returns and claims to have information about a conspiracy against him from within his own administration. Kim and Miguel plan to kidnap Megan from the hospital in order to take her out of LA and away from the nuclear threat.

Jack forces Nina to help with a sting operation against her contact in the hopes that he can lead them to the bomb. Palmer and Mike try to gage Stanton's loyalty when they investigate the chopper crash. George has a final conversation with his son.

Kim and Miguel are arrested and the police plan to take them back to LA. Tony questions Bob Warner at CTU and learns more about his government connections. Palmer discovers a traitor in his ranks when the journalist whom he was holding is set free. Nina pulls a deadly countermove, setting herself up as the main player in the search to locate the bomb.

George pits Bob against Reza in hopes of learning which one is working with Second Wave. Sherry and Lynne clash over Palmer's speech to the press. Kate is interrogated by Syed Ali, who believes she knows too much about the bomb. Jack and Nina fight off a group of renegade soldiers while waiting to be rescued from the crash site. They nearly escape when Nina takes Jack hostage and demands to speak to the President.

Two traitors are uncovered. One is the mole in the Palmer administration who is working with Stanton. The other is the member of the Warner family who helped Syed Ali to bring the bomb into the country. Jack learns of Ali's location and tries to rescue Kate. Kim and Miguel hatch an escape plan to stay out of LA, but the results are disastrous.

Kate helps Jack to locate and identify Syed Ali. Palmer places Stanton under arrest, but he won't break. Palmer realizes he must go to extremes to make Stanton talk. Kim hits her low point of the day when she encounters a cougar in the woods.

Jack engages in a brutal contest of wills with Syed Ali. George questions Bob Warner to learn more about Marie's motivations for helping the terrorists. Kim is rescued by a mysterious hunter who offers her asylum. Lynne receives a dire warning from Sherry.

Jack and his men prepare for a confrontation with Stanton's renegade soldiers as they converge on the bomb. Kim becomes suspicious of her host, but is forced to stay because of her status with the police. Stanton finally breaks down and gives Palmer some unpleasant news.

Jack and Kate try to break Marie's resolve so they can learn the location of the bomb. Palmer confronts his ex wife with the information that Stanton gave them. George finally steps down as director of CTU and hands the position over to Tony. Kim discovers her host's deception.

Palmer, Mike and Lynne discuss various ways to dispose of the ticking bomb. They conclude that the desert is the best place to set it off. Jack determines that one man must pilot the plane carrying the bomb. He chooses to fly the plane himself and bids a tearful goodbye to his daughter. Tony and Michelle become suspicious of a Middle Eastern diplomat who is asking questions about the evidence against Syed Ali. Palmer departs for Los Angeles so he can be on hand when news of the nuclear bomb reaches the public.

Jack and Michelle question Syed Ali, who claims that the audio recordings are false. Palmer prepares to wage war against the three countries who were involved in the nuclear strike. Kim gets caught in a hostage situation. Jack is contacted by a man who wants to exchange information for Kate Warner.

Jack meets with the surviving Coral Snake Commando, who demands Kate Warner in exchange for evidence about the recordings. Tony and Carrie spy on Michelle when he suspects that she is working with Jack. Mike and the Vice-President turn up the pressure on Palmer, when he expresses his doubts about the impending war.

Jack, Kate and Wallace fight to escape from a deadly band of commandos. Palmer decides to take a stronger stance against the civil unrest resulting from the bomb explosion. Tony's trust in Michelle is broken when he suspects her of betraying him. Kim's worries seem to be over when she learns the charges against her have been dropped.

Jack is captured and tortured by men who want the chip. Kate and Yusuf run into a group of angry rednecks before they can deliver the chip to CTU. Tony and Michelle share a tender moment after her brother flips out. Palmer leans towards holding off the attacks, while Lynne discovers a secret operation that the Vice-President is planning against Palmer.

Jack finds an ally who may help him escape from Kingsley's men. Lynne meets with foul play before she can warn Palmer of the conspiracy against him. Chappelle interferes with Tony's efforts to assist Jack. Kate offers her captors money in exchange for the chip.

Palmer's cabinet invokes the 25th Amendment in an attempt to remove him from power. They place him on trial for his extreme actions during the nuclear bomb threat. Jack and Michelle work against the clock to prove that the evidence against the Middle East is false.

Jack locates the man who forged the audio evidence, but his efforts to break him down are sabotaged by Sherry Palmer, who has a hand in the conspiracy. Kim returns to the Matheson home, where she discovers that her problems are far from over. Palmer searches for an ally who will help him get a message out to CTU. Tony and Michelle take Chappelle out of action when he hinders their efforts to help Jack.

When Jack hits a dead end with his lead, he realizes he must persuade Sherry to help him get evidence against Kingsley. Things go awry at CTU when Division becomes suspicious of Chappelle's absence. Michelle goes off-site to work with Jack. Mike and Prescott ask Palmer to aid them as the bombers get closer to their targets.

Jack uses Sherry to lure Kingsley out into the open, but Kingsley suspects a set-up and lays his own trap. Kate and her father have a final, ominous conversation with Marie. Palmer's attorney finds evidence involving Kingsley and convinces Mike to release Palmer from custody. Palmer and his cabinet gather to watch as Sherry meets with Kingsley. Mike orders Chappelle to reinstate Tony and Michelle. Jack sends Sherry in for the meeting with Kingsley, but his mounting heart troubles cause problems for him at the crucial moment.