Jack tells Agent Walker that he thinks her FBI team has been compromised, and convinces her that they need to go after Tony on their own; and President Taylor prepares a US invasion of Sangala.

At air traffic control, supervisor Sid Paulson and his crew realize that someone has hacked their system, and that they've lost contact with GSA flight 117. Agent Walker radios Moss, and tells him about Schecter's death. She says the killer is still in the Columbia Building across the street. Moss says he'll send a SWAT team to aid in the search. Bauer tells Walker he thinks there is a security leak in her office, which would explain how Tony and the assassin knew where they were. Walker can’t believe a member of her team is a traitor. From inside the building the killer (Tanner) sees the influx of agents, and realizes he's trapped. Tony and Masters use the CIP module to redirect GSA 117 and another flight onto a collision course. Tony calls Paulson, and tells him to watch as the two flights begin to land simultaneously on intersecting runways. Helpless, the air traffic controllers watch the planes approach each other. Just before impact Tony contacts the GSA pilots, and tells them to pull up. They do, narrowly avoiding a collision. Tony calls Paulson again, and tells him that was just a warning; next time will be for real.

On a boat harbored at a commercial dock, Tony tells Masters to get the CIP module ready for David Emmerson, who has just arrived. Tony tells Emmerson the test of the module went perfectly; he hands the module (and its creator Latham) over to the man who appears to be the boss. Emmerson asks how the FBI found Schecter. Tony says the Feds are being helped by Jack, but assures his boss that he'll handle Bauer. Tony asks about the next job. Emmerson says Tanner has the specs; for now, Tony knows all he needs to know. In the White House Press Secretary Angela Nelson tells the press corps that President Taylor intends to send troops to Sangala to stop General Juma's genocide, and restore Prime Minister Matobo to power. While Chief of Staff Ethan Kanin is made aware of the near miss at the airport, Taylor meets with Matobo. She makes it clear to the deposed Prime Minister that once Juma has been removed from power, he must be dealt with according to the rule of law. Matobo gives his word to do so. As the SWAT team arrives at the Columbia Building, Tanner calls Tony, saying he's trapped inside; Tony says he'll send help. From outside, Walker and other agents watch video as the SWAT team sweeps the building floor by floor. In the basement of the Columbia Building, Tanner hides while FBI Agent Lennert searches for him. The two men come face-to-face, and Lennert says he was sent by Tony. He gives Tanner his FBI windbreaker, and the keys to a car, and then radios in that the basement is clear. Tanner dons the coat, and heads to the exit. Outside, Bauer spots Tanner walking away from the building. He can tell from his work boots (as opposed to the glossy black shoes worn by the others) that he’s not a real agent. He tells Walker, and she agrees with his assessment. With further proof that the Bureau has been compromised, Jack convinces her they need to tail Tanner on their own… at least until they know who can and can’t be trusted. She agrees, and they follow, hoping Tanner will lead them back to Tony.

At Starkwood Headquarters, Emmerson arrives with Latham and the CIP module. He hands the module over to Colonel Dubaku, who vows revenge on the US for interfering with General Juma, and for the death of his brother Youssou. In the White House Taylor and her advisors discuss the many different ways whoever has the CIP module could attack the country’s infrastructure... ranging from shutting down the national power grid to poisoning the water supply. Kanin's phone rings: it's Secret Service Agent Gedge. Gedge says he is with Henry Taylor, and they are en route to confront Samantha Roth. He says Mr. Taylor believes that Samantha knows more than she's saying about Roger Taylor's death. Gedge says Taylor has been consumed with proving his son didn't commit suicide, and now he is growing increasingly concerned with the First Gentleman’s state of mind. At FBI Headquarters Agent Moss learns that Walker left the Columbia Building without telling anyone where she was going… and that Bauer left with her. Jack and Walker tail Tanner's vehicle. Walker's phone rings: it's Moss. Still concerned about the breach in FBI security, Jack tells her not to answer. She takes the call, but lies about where they are and what they’re doing. After hanging up, a suspicious Moss tells Janis to locate Walker using the signal from her walkie-talkie. In the car Jack tells Walker he is still willing to help her track down Tony, but since the FBI has been compromised, she needs to let him do things his way.

Henry Taylor and his Secret Service contingent arrive at Samantha Roth's office. He presses her about his son's death. She maintains that Roger killed himself, and that is all she knows. He says he knows about the money in her offshore account, but she says it belongs to a relative and not to her. Taylor doesn't believe her, and asks who is buying her silence. She sticks to her story, but he's not convinced. Growing ever more frustrated, he grabs her arm. Agent Gedge intervenes, saying it’s time they leave. Tanner arrives at the commercial harbor, and drives up to the boat. Jack and Walker park their car. She gives him a sidearm, and they follow Tanner on foot. Jack gets the drop on him. With Jack's gun in Tanner's back they approach the boat while Walker takes a different path. Tony's associate Fox sees Jack, and opens fire. Tanner is hit, and collapses. Walker shoots Fox, and the two agents continue towards the boat. Masters appears, and shoots at them but misses. They turn, shoot, and hit their mark. Jack and Walker board the boat. Walker finds Masters' laptop, but all the files have been deleted. Below deck Jack finds Tony, who manages to escape topside. Jack pursues, and has Tony in his sights. He stops Tony with his voice, but then hesitates. Tony seizes the opportunity, and leaps to the dock. Jack does the same, dropping his gun as he does. The two former CTU agents grapple and fight, but Jack gets the upper hand. Walker emerges from the boat, and says the CIP module is gone. Jack asks Tony where it is, but he remains silent. An FBI helicopter approaches, and Walker looks up to see Moss on board. Jack looks at Tony, and wonders what happened to his old friend.