Air date: 4/6/09
Before retreating from the compound, Larry creates a diversion by punching Seaton so that Tony can sneak off and remain on the compound covertly while the FBI and Navy SEALS teams pull out. Jack becomes symptomatic and must decide whether to involve his daughter, Kim, whose stem cells could cure him. Olivia blackmails a reporter to keep the crisis from going public. Tony locates the bioweapons with the help of a Starkwood insider, Doug Knowles, who had been assisting Senator Mayer's investigation into Starkwood's activities. This prompts President Taylor to order an air strike on the facility. Knowles is subsequently captured and taken to Hodges, who bottles him to death. Hodges learns of the strike and threatens to launch the pathogen, forcing the President to abort.
1:00 AM – 2:00 AM
Air date: 4/13/09
The President meets with Hodges and Seaton, who declare that they will release the pathogen if Starkwood is not given a greater role in US military operations. As part of a covert operation deniable by President Taylor, Tony destroys the compound holding the pathogen and missiles, prompting the President to arrest Hodges and Seaton. Kim reunites with her estranged father, Jack, when he reveals his exposure to the bioweapon. Larry and his teams secures the Starkwood compound, but an operative named Galvez escapes with a canister of the pathogen. During the ensuing chase and firefight, the Starkwood operative shoots and wounds Larry. Tony betrays and smothers Larry before checking the canister and ordering the operative to take it somewhere safe.
2:00 AM – 3:00 AM
Air date: 4/20/09
Galvez hides inside the FBI perimeter while Tony shoots himself to mask his involvement. Renee and Jack are informed of Larry's death and join the FBI team searching for Galvez. Tony plans to trap the FBI team in an empty apartment building and use C4 to demolish it, creating a diversion so Galvez can escape. Meanwhile, an unknown figure, Cara Bowden, impersonates Hodges' lawyer to lecture him that the bioweapon was not meant for Hodges' personal use, and threatens his family unless he commits suicide to preserve the identity of his co-conspirators. Galvez poses as an FBI agent and lures the team into the building. Jack realizes via tracking devices that the agent Galvez is impersonating is away from the building; Jack warns Renee, but the building explodes before the team can escape. Walker is unharmed, but a suspicious Jack learns that Tony lied to him regarding his source on the White House raid. With all evidence pointing to Tony's involvement, Jack confronts Tony, but has a seizure, allowing Tony to escape. Hodges consumes the suicide capsule handed him by Cara and is rushed to the hospital. Tony escorts Galvez and the pathogen to an ambulance, which Galvez promptly hijacks.
3:00 AM – 4:00 AM
Air date: 4/27/09
Jack reveals to Renee that Tony is working with Galvez and was involved in Larry's death. Tony pays Galvez for the canister, but he refuses to deliver it and instead pulls a gun on Tony. Galvez demands the name of the buyer but Tony manages to overpower and kill him. Tony meets up with Cara Bowden who posed as Hodges' attorney and they set up a video conference with their conspirators. The anonymous conspirators reveal that they had planned to use the bioweapon six months later, at which point the country would be thrown into disarray and the group could assume control of the government. Realizing that Hodges' ill-timed action actually made this plan viable immediately, they decide to use the last canister to launch another attack on the US and frame a Muslim terrorist cell. Hodges, stabilized at a hospital, brokers a deal for witness protection, much to Olivia's disapproval. In return, Hodges tells Jack about the impostor and the shadow conspiracy. President Taylor authorizes the use of decommissioned CTU servers and Chloe is asked by Jack to manage the servers. Meanwhile, Tony, Cara and a team kidnap a Muslim scapegoat for their operation while Jack begins to display signs of dementia.