As the day stretches into the middle of the night, Jack and the FBI formulate a plan to prevent further terror attacks; events take an unexpected turn when the politics surrounding the administration expand beyond the White House.

As Tony and Moss realize that this was a trap, Hodges confronts the FBI team and orders them off his property. There are no weapons of mass destruction here. He gives them five minutes to leave, and demands Seaton's release. Back at FBI HQ, Agent Walker and Jack confer. Jack finds another contact inside Starkwood, Douglas Knowles, who was cooperating with Senator Mayer's investigation. Jack calls Knowles at his office, and he's relieved to hear from the FBI. He thinks he knows where the canisters are. Jack calls Tony and Moss: the FBI should withdraw, and find a way to leave Tony behind to meet up with Knowles. Moss creates a diversion by insisting on arresting Seaton, and then getting into a fistfight with him. Tony slips away during the scuffle. A Starkwood commando puts a gun to Moss' head, and Moss backs off. He and the rest of the SWAT team leave. Tony finds Knowles, who says the weapons are likely in a secure area. He has no idea how they'll get there without being caught. Tony calls Jack for support, but Jack's starting to tremble and shake. The bioweapon is starting to affect him. Janis takes over, providing satellite support, and tells them they can proceed. Jack's trying to hide his symptoms, but Agent Walker has noticed and is worried. They call the President, who is appalled that Starkwood was prepared to fire on Federal agents. She's willing to order a surgical air strike on Starkwood, but only once she has visual confirmation of exactly where the canisters are. Since Jack's the only one who has seen them, the confirmation has to come from him.

Olivia gets a call from TV reporter Ken Dellao, who has heard rumors that the Joint Chiefs of Staff were called in. He's got a source from Port Authority telling him something about weapons of mass destruction. He demands to know what's going on, and threatens to make Olivia's unseating of Ethan Kanin his top story the next morning if Olivia doesn't talk. They arrange to meet in a room at the Roosevelt Continental hotel.

Knowles leads Tony to the general area where security has been beefed up. Of all the buildings in the area, there's one that Jack sees no infrared signature from; that building must have blackout shielding, and is therefore probably where the canisters are. Knowles distracts the guard by demanding to be let in as Chairman of the Board, claiming he's just out for a walk. As Tony slips inside, Knowles is detained by the guard, who is under order from Hodges to clear away all "non-essential" personnel. As Tony moves deeper into the building, Jack suddenly starts to tremble and shake violently. He then collapses to the floor, shaking and unable to speak.

When Hodges learns about Knowles, he orders him taken back to his office and kept comfortable until Hodges arrives. He also orders a double-down on security with a half-hour until the weapon is ready. Olivia meets with Ken; she tells a reluctant Aaron Pierce to wait in the hallway. She then tells Ken what's going on, and that he needs to kill the story so as not to cause a panic. He agrees...on the condition that she sleep with him. She tells him their relationship is over, but he insists. She reluctantly lets him begin to kiss her. Back at FBI HQ, Jack is given an injection to temporarily control his symptoms. He needs to take another shot at least once every two hours. The bioweapon is more virulent than they thought; however, it turns out that there have been recent medical experiments that suggest a possible treatment. There's a slight chance of a cure if they can use stem cells from a genetically compatible donor. The only candidate is Jack's daughter Kim. Jack, to Walker's bewilderment, refuses to contact her. He returns to his post at Janis' terminal, and warns Tony of a security detail heading towards him. Tony makes short work of the commandos, and switches clothing with one of them. He rides an elevator downwards with Dr. Chapman, the lead scientist, and his disguise works. He reports back that he's four stories down; Janis says they have no information on subterranean floors for that building. Staying out of sight, he manages to get a video feed to them, and Jack IDs the canisters. They'll alert the White House. The place will be dust in ten minutes; time for Tony to get out of there. Hodges meets with Knowles, who demands to know what's going on. Hodges admits everything. He's angry that the country he was asked to defend, who never cared how he got things done, is suddenly asking questions and holding him accountable for his methods. Knowles tells him he can't take on the Federal government. Hodges sadly reflects that for twenty years he's treated Knowles like a son. He expected and deserved a little loyalty. Then he suddenly bludgeons Knowles with a decanter, and throws him off the balcony, killing him. As Hodges attempts to wipe the bloodstains from his shirt, Seaton calls. Radar shows a squadron of F-18s heading their way; ETA, ten minutes. They have three canisters loaded and ready. Hodges says to put in a call to the President. He'll be there momentarily.

At the hotel Olivia is getting dressed. All she cares about is that Ken not write the story... but he says he's going to anyway. The story will make his career. Olivia reveals that she's filmed their lovemaking with her cell phone. If he runs the story, or ever tries to blackmail her again, she'll let the world - and his wife - know just how he gets his leads. She tells him to find a new beat; she doesn't want to see him around the White House ever again. As she leaves, the President calls and tells her to get back to the White House immediately. In the Situation Room Admiral Smith tells the President that Starkwood has a phased-array radar system. They know they're coming; however, they seem to have no anti-aircraft capability. Just then Tim Woods tells the President that Jonas Hodges is calling... and wants a private conversation on a proprietary line he's established. The President takes the call alone in the Operations Room. Hodges tells her he's got three missiles ready to launch at cities on the eastern seaboard, and proves it by showing her the missiles. He wants her to turn the planes around, and to have a private conversation with him at the White House within the hour. Until then, it's to both their advantages that the American people not know the exact nature of their standoff. He gives her thirty seconds to comply. Aghast, she races back to the Situation Room and orders the air strike aborted, which Admiral Smith does reluctantly. All eyes are on the President, uncomprehending, but she cannot risk explaining herself to them. She meets their eyes... and then leaves the room.