The plane carrying Jack and Nina is shot down and together they must fight off a group of soldiers. Mason plays Bob Warner against Reza to find out which one working with the terrorists. Kate Warner is captured and interrogated by Syed Ali. Mason reveals the truth of his condition to Tony.
Jack is captured by Nina Meyers and used as leverage in an attempt to get a presidential pardon. President Palmer learns the identity of one of the conspirators in his administration. After being set free, Reza learns the identity of the person who set him up when he goes to get incriminating evidence on Bob. Jack begins to suspect the soldiers who shot him down were with the NSA as he heads to capture Syed Ali.
Kate Warner leads Jack on mission to locate and id Syed Ali. President Palmer places Stanton under arrest and makes an out of character decision on how to handle the interrogation. CTU discovers that Marie killed Reza and the two agents trailing him.
Jack tries to get information out of Syed Ali. Mason gets Bob Warner to reveal some previously classified history on Marie that paints Reza's murder in a new light. Lynne Kresge becomes suspicious of Sherry.
Jack discovers the bodies of six additional Coral Snake Commandos as a Tactical Team gets closer to the bomb's location. Division sends in Brad Hammond to look into CTU LA's situation. Stanton finally reveals that he has known about the bomb all along and allowed it be smuggled into the country.
Jack gets back to CTU after the bomb exploded. The situation there is tense since Tony became head of the Unit, especially when a key witness is assassinated. President Palmer and his staff prepare a retaliation on the three countries involved with Ali.
Jack and Kate leave CTU to meet with the lone surviving member of the Coral Snake Commandos who says he has evidence that the tape is fake. President Palmer wants to wait and see what Jack finds out before launching a retaliatory strike.
Jack, Kate, and Yousef try to get Wallace to a hospital after he gets shot by unknown assailants. President Palmer tries to deal with civil unrest as Muslim communities across the country are targeted.
Jack is captured by a group of men working for an oil magnate named Peter Kingsley who's looking to capitalize on the coming war. Lynne Kresge discovers that Vice-President Prescott is planning on seizing the presidency by way of the 25th Amendment. President Palmer deals with some increasingly impatient Joint Chiefs of Staff. Kate and Yusef are attacked by angry American citizens when they try to get the chip behind the Ali recording back to CTU.
Jack tries to escape from the Kingsley's men after being tortured. Lynn Kresge tries to warn President Palmer about VP Prescott. Regional Director Ryan Chappelle returns to CTU and exerts his authority. Kate tries to retrieve the stolen computer chip. President Palmer begins to suspect something is wrong when Prescott won't return his phone calls.
After saving Kate from her attackers Jack heads to meet Alex Hewitt who may be the person who designed the computer chip. President Palmer's ability to the run the country is questioned when the Vice-President and members of the cabinet invoke the 25th Amendment.
Jack has Sherry contact Peter Kingsley who turns out to be the mastermind behind the tape. Mike Novick realizes that he has made a huge error in judgment in supporting Prescott. Deputy Regional Director Brad Hammond places Tony and Michelle under arrest.
Jack and Sherry head to LA Coliseum to meet Peter Kingsley. Upon hearing evidence via the live audio feed, President Prescott aborts the air strike. David Palmer is reinstated as President, and speaks to the nation about the nuclear bomb.
Three years later; CTU receives a threat that Mexican drug lord Hector Salazar is planning on releasing a deadly contagious virus in LA unless Jack gets his brother Ramone Salazar out of prison. President Palmer prepares for a presidential debate with Senator John Keeler.
After Goss' infected body is dropped at the hospital Jack and Chase begin to trace his last known locations while CTU tries to figure out how the virus is gonna be unleashed to the public at large. Once they figure out it's gonna be spread through cocaine shipments CTU begins to track down drug dealers in East LA. President Palmer considers canceling the debate.
Tony and one of Salazar's cronies close in on a young drug trafficker who may be unknowingly carrying the virus. Jack informs Kyle Singer's parents that he may be infected. Wayne becomes concerned over David's latest affair when he learns the woman's ex-husband will perjure himself over sworn testimony he gave years earlier unless the President pays him not to.
In order to get Ramon out of prison Jack asks for President Palmer's permission to instigate a prison riot. Michelle takes over command of CTU after Tony is injured. Chase disobeys orders and fiercely interrogates Roman as Jack puts his plan into motion. President Palmer has Wayne call off the meeting with Anne's ex-husband. Drug dealer Kyle Singer is captured by Salazar's men.
Jack and Ramon are captured by dangerous prison inmates after trying to escape. President Palmer begins his debate with Senator Keeler. At CTU, Chloe O'Brian discovers evidence of Jack's heroin addiction.
Jack and Ramon try evade military helicopters when they make a run for a plane scheduled to leave for Mexico. Palmer cancels the debate. Kyle Singer learns that he is not infected with the virus. Kim discovers that Gael Ortega might be working with the Salazars.
Ramon holds Jack hostage as they fly down to Mexico. Regional Director Chappelle interrogates Gael; Tony returns prematurely to CTU to reveal Gael's true allegiance. Chase disobeys orders and heads for Mexico to rescue Jack.