Michael Latham, an engineer who was abducted, is in a warehouse being forced to work on a firewall module by a man named Masters. Meanwhile, Jack gives testimony to a Senate Hearing in Washington, D.C. about human rights violations by the recently disbanded CTU. He answers questions posed by Senator Mayer but refuses to regret the choices he made as a CTU agent because he only did what was necessary to prevent terrorists from killing innocent people.
The hearing is interrupted by FBI Agent Renee Walker. She has a subpoena to obtain Jack immediately. At FBI headquarters, Agent Larry Moss briefs his team while analysts Janis Gold and Sean Hillinger prepare for Jack's arrival. Masters monitors air traffic control systems about a flight headed for New York. When Jack arrives at FBI, Larry explains that they need his help with an investigation. The CIP firewall protecting the national infrastructure might be breached. Renee shows Jack that one of the men behind the threat is Tony Almeida. Jack cannot believe that Tony is still alive. Apparently, Tony was rushed from CTU after Jack saw him "killed." Tony enters the warehouse and Masters tells him that they have accessed air traffic control, but their CIP module is spotty.
Tony orders Latham to make the module work or else they will kill him. In the Oval Office, President Allison Taylor watches newscasts about General Juma's "ethnic cleansing" in Sangala, Africa. She discusses with her Chief of Staff Ethan Kanin that she is adamant to send troops in to stop Juma. Taylor's husband Henry doesn't think the invasion will go over well with the press and he offers to handle a reporter. Ethan privately tells the President that Henry may not be up to the job because he's still not over the death of their son, Roger. Latham gets the module to work. FAA air traffic controllers notice a blip in their system.
Renee thinks that Tony is angry about his wife's murder and wants justice. Jack is sure that there is a logical explanation, but he agrees to help the FBI find Tony. Word of the air traffic control interception comes in, and the FBI notifies the White House. In the White House situation room, President Taylor argues with her generals and cabinet members about the invasion. She is interrupted with news about the FAA breach. Taylor is suspect about the timing of this event and her decision on Sangala. Henry receives a call from the private investigator he hired to look into Roger's "alleged" suicide. Roger's girlfriend might be hiding something and Henry wants to talk to her personally. Henry asks his Secret Service tail Agent Gedge to escort him somewhere and keep it off the manifest.
With full access to the FBI intelligence, Jack realizes that Tony must have forged an access card and may have used an old CTU informant named Schecter, who is in Washington. Jack knows that Schecter will call his lawyers if the FBI goes in with a warrant. Larry accuses Jack of wanting to resort to his torture methods instead. Renee offers to accompany Jack to see Schecter. She promises Larry that she will keep Jack on a short leash. Jack and Renee go to see Schecter, who knows what Jack is capable of. Schecter claims he doesn't know that Tony is alive nor did he help steal a device to breach the firewall. Renee tries to bargain, but Schecter refuses to budge. Jack grabs the gun from Schecter's bodyguard and holds Schecter at gunpoint to find out about Tony. Renee begrudgingly gives Jack the go-ahead to "do whatever it takes." Schecter is in fear when Jack holds a ballpoint pen to his eye. Schecter is about to tell them about Tony when shots fire through the window. Schecter falls dead.
The phone rings, and Jack answers. It's Tony, who tells Jack to stay away. The flight to New York begins to descend as the FAA controllers lose communication with its pilots. Yet the pilots don't know anything is wrong. Tony speaks to them as if he is an air traffic controller. He instructs Masters to change the flight's course.