Air date: 3/9/09

Jack informs Bill that he released enough natural gas in the safe room to create an explosion. As the President reads a statement apologizing for the invasion of Sangala, Bill tells Jack that he saw Juma on the phone with another co-conspirator; Bill then grabs a guard's weapon and sets off the explosion, killing himself and several of Juma's henchmen. In the chaos, Larry orders an assault against the Vice President's wishes, and Jack and Aaron secure weapons and eliminate Juma and his men. The President appoints Olivia to an advisory position in an act of reconciliation. Jack informs Larry of the other co-conspirator and asks to interrogate Burnett again without using torture. Larry refuses and orders Agent Powell to arrest Jack, but Renee convinces Ethan Kanin, the President's chief of staff, to override Larry. Consquently, Larry suspends Renee for insubordination and accompanies Jack to the hospital. As Jack begins the interrogation, an assassin sent by Juma's co-conspirator, Hodges, briefly disables the camera and audio feed to the hospital room and immobilizes Jack and Burnett with nerve gas before slitting Burnett's throat, framing Jack for the murder. After recovering, Jack steals the security tapes and escapes the hospital with the FBI on his tail.

9:00 PM – 10:00 PM

Air date: 3/16/09

Jack sends a photograph of Burnett's killer to Renee. She identifies the man as John Quinn, an operative for a private security company called Starkwood, which is being investigated by Senator Mayer. Jack travels to Mayer's residence, and they discover that Starkwood helped Juma attack the White House in exchange for an unmonitored area in which Starkwood could develop and test a biological weapon. Larry discovers that Renee contacted Jack, and orders her arrested. Morris O'Brian decrypts Renee's messages to Jack in exchange for immunity for Chloe. Meanwhile, Quinn arrives at the house, kills Mayer, and pursues Jack to a construction site. Jack kills Quinn, whose cell phone messages reveal that the weapons have arrived at a nearby shipyard. The FBI arrives at Mayer's residence to find him dead; Larry assumes that Jack is the culprit.

10:00 PM – 11:00 PM

Air date: 3/23/09

At the shipyard, Jack and Tony question a port authority guard and discover that a group has arrived to collect the bioweapon. They follow the operatives to a container, but Jack starts a firefight when they attempt to kill the guard. Jack commandeers the truck carrying the weapon, but Tony is captured by the operatives. Larry finds evidence of a third person at Mayer's house, and Renee tells him about Jack's investigation of Starkwood. At the White House, Ethan resigns to shoulder the blame for Jack "murdering" Mayer, as well as in response to threats from Olivia. Henry leaves surgery and expects to make a full recovery, while Olivia leaks information about Ethan's resignation to the press. Jack tells Larry to send a team to rescue Tony and to retrieve the weapon before the operatives catch up to Jack. However, Jack is forced to stop a leak in the weapon, giving the operatives time to catch up and recover it. Jack notifies Larry that Starkwood has reclaimed the weapon and that he has been exposed to it.

11:00 PM – 12:00 AM

Air date: 3/30/09

Jack is placed in quarantine due to his exposure to the bioweapon. President Taylor appoints Olivia temporary Chief of Staff and is briefed on the situation with Starkwood. Taylor concludes that a direct assault on the Starkwood compound would yield the fewest casualties. Jack's blood work confirms he is infected; he is placed in a medical room and debriefed by a sympathetic Renee. At the compound, Hodges obtains the bioweapon and attempts to extract information from Tony regarding agency knowledge of the weapon. Hodges' adviser, Seaton, shoots the operative interrogating Tony and offers to reveal the bioweapon's location for immunity. With that, FBI tactical units and U.S. Navy SEALs, with Larry, travel to the compound. However, the weapon is not at the provided location; Seaton bluffed to buy Hodges time to prepare the bioweapon. A battalion of Starkwood operatives, including the one supposedly killed by Seaton, surrounds the FBI/Navy team with Humvees and threatens to fire if they move.