A snag in the sale of the virus leads the Salazars to question Jack's motivations and as a result they put his allegiances to the test. Claudia works to help Chase escape after Jack informs her of his real priorities. Tony's ability to run CTU is called into question. Palmer is put into a difficult position regarding his brother.
In order to get closer to the virus, Jack tries to make Nina believe he still has feelings for her. Wayne tries to gain the trust of Julia Milliken when Alan Milliken starts making demands. Chase convinces Salazar's girlfriend to help him escape.
Jack and Nina prepare to meet with Amador, the man selling the virus; CTU organizes an ambush. Ramon and Hector have a falling out. President Palmer asks his ex wife Sherry to help with the Milliken situation.
Nina releases a deadly computer virus into CTU's systems after getting captured by Jack and Chase. Sherry runs out of options and decides to directly confront Alan Milliken but things go too far. Chloe and the rest of the tech crew work overtime to combat the virus.
Regional Director Chappelle forces Jack to undergo a medical evaluation for his heroin addiction. Tony interrogates Nina Meyers. Julia Milliken confronts Sherry after Alan dies while Wayne and President Palmer prepare for the fallout. Nina tries to escape custody after collapsing during the interrogation.
Amador and his people receive orders from their client to release the virus in the Chandler Plaza Hotel. Jack closes in on Amador but it's too late. Michelle and Gael alert the Chandler's Chief of Security to the dangers of the threat.
After the interrogation goes nowhere, Jack and Chase let Amador escape hoping he will lead them to his client's location. Michelle places the hotel under quarantine and must make a difficult decision in how to handle the ensuing panic. President Palmer is put into a awkward position when handling the Milliken situation.
President Palmer gives into Stephen Saunders's strange demand of placing an seemingly nondescript phrase into a speech in the hopes of delaying another viral outbreak. Michelle takes control of the situation inside the hotel. Jack and Chase bring a suspect to the local branch of MI-6 as Saunders launches an attack on the building.
Jack has to comply with another one of Saunders' demands: the death of Regional Director Ryan Chappelle. Michelle discovers that one of the infected hotel patrons got out before the quarantine was enforced.
When CTU learns that Saunders has a daughter attending an LA university they must inform Jack the only match for a bait and switch operation is Kim Bauer. Chase tracks down the man who escaped the hotel quarantine. Palmer informs his cabinet on the dangers of the threat.
Jack works on using Saunders' daughter in an attempt to gain control of the virus. Michelle waits to find out if she's infected. Palmer navigates around a angry and confused press. Saunders starts making demands on Tony.
Tony works covertly to find a way to get Janes Saunders out of CTU and deliver her to Saunders before Jack and Chase find him. Senator Keeler receives some damaging information on President Palmer from a surprising source.
Jack and Tony clash as they wait for the time of hostage exchange with Saunders. Senator Keeler confronts President Palmer about the Milliken cover-up while Wayne initiates a secret operation against Sherry.
Jack and Chase corner Saunders' henchman Arthur Rabens in an active public school. Tony faces losing command of CTU and treason charges for saving Michelle. An emotionally broken President Palmer decides to drop out of the race for reelection.
In the closing moments of Day 3, Jack Bauer gets into his car and breaks down in tears after everything he has endured. He gets a call to report back to CTU, and, after a moment, acknowledges and drives away.