Day 3 sees CTU deal with a deadly virus threat that would be released in Los Angeles. We again see the return of Jack’s nemesis Nina Myers just as he is trying to overcome a heroin addiction after his undercover operation with Ramon and Hector Salazar, as others feel he still has not gotten over the death of wife Teri at the end of the first season. Jack has a new protege in tow, Chase Edmunds, but things take a turn for the worst when it is revealed Chase is seeing his daughter Kim, and it causes tension among the three of them.
President Palmer is seeking re-election against Senator John Keeler, but his campaign turns sour after one of his major backers, Alan Milliken, discovers Palmer’s brother, Wayne, has been sleeping with Milliken's wife, Julia. Palmer's campaign suffers a major blow when revelations come out about his girlfriend and personal physician Anne Packard. The president turns to his ex-wife Sherry to deal with Milliken. She takes it all a step too far as she kills Milliken by not allowing him his medication, which he needs to stay alive. Despite David Palmer's best cover-up efforts, Keeler uses it as leverage in the campaign. Towards the end of the day, Julia kills Sherry before taking her own life. Palmer decides soon after to not seek re-election.
Back at CTU, it turns out that Tony Almeida, Gael Ortega, and Jack have been working undercover on a sting operation. Chase is initially unaware of the situation and attempts to “rescue” Jack, who is being held captive by the Salazars. Tony recovers from a gun shot wound to the neck, to return as head of CTU, with many doubting his abilities.
Nina comes in just as Jack and the Salazars are trying to get hold of the virus from Michael Amador, but he plays them all for fools. After Nina is captured by CTU and interrogated, she tries to commit suicide but fails. She then escapes CTU only to be found by Kim before Jack comes in and finally gets revenge for the death of his wife Teri.
Amador meets with his accomplice Marcus Alvers, who has planted some of the virus in a hotel ventilation system, as well as with the man behind the terrorist strike, Stephen Saunders. Gael is killed soon after being exposed to the virus which he was trying to prevent being released into the hotel's ventilation system, and Michelle has to deal with the threat at the hotel, as well as the unruly guests who soon discover the deadly truth.
Saunders contacts President Palmer and gives him a series of assignments, one of which he carries out successfully. The other task, however, is to kill Regional Division Director Ryan Chappelle. Jack and Chase try desperately to capture Saunders, but in the end Jack is forced to kill Chappelle and hand over his body as proof.
Once Saunders has been captured, Jack uses all means possible to stop the threat posed by the remaining vials, which eventually leads to Chase agreeing to let Jack cut off his hand because Chase had attached the virus-delivery device to his wrist to secure the vial. Physicians are attempting to reattach his hand as the season draws to a close.
The final scene of season 3 shows an emotional Jack Bauer having a minor breakdown as a result of the day's events until he is once again enlisted by CTU to interrogate one of the day's suspects. The day ends with Jack on his way back to CTU and back to work.
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