Day 7 begins in a U.S. Senate hearing during which Jack Bauer defends the necessity of his actions to Blaine Mayer. Renee Walker postpones the proceedings saying that the Federal Bureau of Investigation (FBI) urgently needs Jack's help. Even though Jack refuses to believe it at first, she reveals that Tony Almeida is still alive and that he is launching an attack against the government that betrayed him. When a contact agrees to talk to Bauer and Walker and is assassinated, the sniper leads them to Tony's location. Jack captures Tony and brings him to the FBI but learns that he is part of an undercover operation involving Bill Buchanan and Chloe O'Brian that aims to expose corruption in the government.
Jack breaks Tony out of the FBI's headquarters and meets with Bill and Chloe at a hideout that serves as a sort of underground CTU. There, he learns that Benjamin Juma and Ike Dubaku have infiltrated the government in order to a stop the U.S. from invading Sangala. Dubaku plans to attack government infrastructure using the "CIP device" and have the Sangalan President, Ule Matobo, kidnapped. Jack and Tony team up with one of Dubaku's contacts, David Emerson and proceed to kidnap Matobo. Along the way, Renee Walker discovers them. Instead of killing her, Jack manages to keep his cover safe by shooting her in the neck, burying her alive and sending her location to Chloe and Bill. After Tony reluctantly kills Emerson, the group hand Matobo over to Dubaku's henchmen and begin an assault once they learn Dubaku's location. During the assault, they rescue Matobo and destroy the CIP device but Dubaku escapes.
Dubaku attempts to manipulate President Taylor by kidnapping Henry Taylor but Jack and Renee find the First Gentleman by interrogating a U.S. Secret Service agent. During the rescue, Henry Taylor suffers a gunshot wound from which he eventually recovers. With Dubaku on the run, Walker and Bauer are able to find him with the help of his girlfriend Marika. Although Dubaku's vehicle crashes in a car chase killing Marika, Dubaku survives with enough strength to provide Bauer with a list of names of his co-conspirators. Buchanan uses this list to begin making arrests. When the arrests are in progress, Tony informs Jack that General Juma is planning an attack and tells him that a man named Burnett in the White House knows the details. Jack begins to torture Burnett but he is apprehended before he can finish. Juma is able to attack his target - which turns out to be the White House - and Jack, Bill and Allison find themselves held hostage.