As Tony and Larry 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 the FBI, Renee and Jack confer. Jack finds another contact inside Starkwood named Douglas Knowles who was cooperating with Senator Mayer's investigation. Jack calls Knowles, who is relieved to hear from the FBI. He thinks that he knows where the canisters are. Jack calls Tony and Larry, urging them to have the FBI withdraw and find a way to leave Tony behind to meet up with Knowles.
Larry 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 Larry's head, and Larry backs off. He and the rest of the SWAT team leave. Tony finds Knowles, who says that 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 gives them the go-ahead to proceed. Jack's trying to hide his symptoms, but Renee has noticed and is worried. They call the President, who is appalled that Starkwood was prepared to fire on federal agents. She is willing to order a surgical air strike on Starkwood but only when she has visual confirmation of exactly where the canisters are. Since Jack is 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 has a source from Port Authority telling him something about weapons of mass destruction. Dellao demands to know what's going on and threatens to make Olivia's unseating of Ethan Kanin his top story the next morning if she 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 where the canisters are probably located. 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. Tony moves deeper into the building. Jack suddenly starts to tremble and shake violently, and then collapses to the floor, unable to speak.
When Hodges learns about Knowles, he orders him taken back to his office and kept comfortable until he arrives. Hodges also tells him to double down security with a half-hour until the weapon is ready.
Olivia meets with Ken, and has a reluctant Aaron Pierce wait in the hallway. She then tells Ken what's going on and asks that he kill the story so as not to cause a panic. He agrees, on the condition that she sleep with him. She insists that their relationship is over, but he won't relent. Olivia reluctantly lets him begin to kiss her.
At the FBI, Jack is given an injection to temporarily control his symptoms. He needs to take another shot at least once every two hours because the bioweapon is more virulent than they thought. However, 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. To Renee's bewilderment, Jack refuses to contact Kim.
Jack returns to his post at Janis's 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 lead scientist Dr. Chapman, and his disguise works. Tony reports back that he is 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 will alert the White House. Since the place will be dust in ten minutes, it's 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 warns him that 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. Hodges then 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 are heading their way and will arrive in 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. However, 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. Olivia suggests he find a new beat because she doesn't ever want to see him around the White House again. As she leaves, the President calls to order her back immediately.
In the Situation Room, Admiral Smith tells President Taylor that Starkwood has a phased array radar system and knows that they are coming. Yet 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 says he has three missiles ready to launch at cities on the eastern seaboard, and proves it by showing her the missiles. He demands that she turn the planes around. He also wants a private conversation 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, President Taylor 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.