Day 4 begins with the bombing of a commuter train which (unbeknownst to CTU at the time) enables the theft of a device known as the Dobsen-type Override which could be used to take control of (and
melt down) United States nuclear power plants. With Jack Bauer working for Secretary of Defense James Heller, his job brings him to CTU as a visitor on this very day.
Believing that something terrible is about to happen, Jack begs CTU director Erin Driscoll to reinstate him and begins to interrogate a suspect. The suspect reveals that James Heller and Audrey Raines are the primary targets just as they are kidnapped. When Jack saves a civilian programmer who discovered evidence of a cyber-attack in progress (a friend of Chloe O'Brian), he allows one of the terrorists to escape and lead him to where Raines and Heller are being held. Even though Jack rescues them, the mass
streaming of the planned execution video gives the terrorists the opportunity they need to launch an attack on the firewalls and begin using the override.
CTU finds out about the override with the help of Bauer and Tony Almeida and identifies the man responsible for using it: Habib Marwan, an employee of the defense contractor that developed the override. Marwan is able to sabotage one plant, the San Gabriel Island reactor, before Jack's team puts him on the run. Seeking extra intelligence, Bauer and Paul Raines (Audrey's ex-husband) travel to the headquarters of the defense contractor McLennan-Forrester. However, in an effort to cover up their complicity and erase computer records, McLennan-Forrester activates an
EMP, causing a blackout over an 8-square-mile (21 km2) section of downtown Los Angeles.
McLennan-Forrester sends mercenaries after Bauer and Raines. They critically injure Raines just as agents arrive sent by Tony Almeida and Michelle Dessler. The resulting turmoil allows a stealth fighter to be stolen from an Air Force base in Southern California. The pilot of the fighter shoots down Air Force One, which crashes into the Mojave Desert, almost killing
President Keeler in the process. Vice-President Charles Logan takes over for Keeler and seeks the help of David Palmer, when the role proves too much for him. Ultimately, Marwan's terror cells steal the nuclear football from the Air Force One crash site and they attempt to use it to commandeer a nuclear missile in Iowa.
Chloe nearly loses her life finding a lead about the missile. It leads Jack to a complicit Chinese national, Lee Jong, hiding at his nation's consulate in Los Angeles. When negotiations break down, Jack leads a clandestine raid against the Chinese consulate and kidnaps Jong. Poorly placed shots by Chinese guards kill the Chinese consul and injure Jong. Paul Raines dies in surgery when Jack insists that saving Lee Jong is a priority. This destroys his relationship with Audrey Raines. The nuclear missile is subsequently launched and CTU begins a last-ditch effort to discover its trajectory and intercept it. As Jack closes in on Marwan and the missile's location, Chinese agents find proof that Jack Bauer invaded their territory. To prevent American secrets from falling into Chinese hands, government officials propose that Jack be conveniently killed.
In a reversal of the events of
Day 1, David Palmer warns Bauer of the attempt on his life, shortly after the nuclear missile is shot out of the sky. In response, Bauer fakes his own death with the help of Tony Almeida, Michelle Dessler and Chloe O'Brian. When Bauer is safely outside CTU, he says a final goodbye to his friend and president David Palmer. He then leaves his old life behind and disappears into the sunrise.