The CDC arrives to test Jack and find out what he may have been contaminated with. He is not yet showing any symptoms. Jack tells them what little he can about the bioweapon. It will take 15 minutes to find out whether he's infected. In the meantime, he asks to be taken to the FBI.
The deadly canisters arrive at Starkwood -- as does the captured Tony Almeida. Hodges demands that the bioweapon be ready to deploy ASAP because two hours is too long. Tony is roughed up, and Hodges promises that he will get out of this alive if he talks. Tony keeps mum. Greg Seaton interrupts; he thinks the plan should be called off now that the government knows because it was supposed to be covert. Hodges angrily tells him to keep his doubts to himself.
At the White House, Olivia recommends a man named Rick Berman from the private sector to replace Ethan Kanin as Chief of Staff. President Taylor says that she wants Olivia to be the provisional Chief of Staff during the search. Olivia is reluctant, but accepts. Larry Moss calls the President to tell her that Jack is innocent, and that Starkwood was involved with today's terrorist attacks. They are preparing to strike right now, so Larry asks for permission to move on Starkwood immediately. The President calls for the Joint Chiefs to be assembled.
Larry releases Renee from holding because he wants her to be the one to debrief Jack. He apologizes for not trusting her, and she apologizes for not trusting him as well. Meanwhile, Olivia meets with Aaron Pierce and asks him to be the agent in charge of her security detail Although she will arrange for his reinstatement, he's reluctant. Before he can give a final answer, she's called into the meeting with the Joint Chiefs. The bioweapon has been identified as an agent that attacks the brain and nervous system and kills within a day or two. There is no cure. Unfortunately, there are no good and legal ways of moving on Starkwood with military force. It would take Congressional approval. The President insists on finding a way.
Tony continues to refuse to talk. Just as Stokes is about to shoot Tony, he is shot dead by Greg Seaton. Seaton thinks Hodges has lost his mind, and he frees Tony. The two sneak into Seaton's office, when Hodges calls. Seaton claims that Stokes is still trying to get Tony to talk. Hodges wants Seaton on deck, ASAP. As soon as Hodges is off the phone, they call Larry at the FBI. Seaton wants immunity in exchange for the location of the bioweapon canisters. Larry needs to run this by the President. While they are waiting, Larry updates Tony on Jack's condition.
In the CDC van en route to the FBI, the results of Jack's blood work come in. Jack reads the diagnosis, his face unreadable. He arrives at the FBI, where Renee is surprised to find that he's not in quarantine. Jack is indeed infected, but he's not contagious.
President Taylor and Olivia watch horrific footage recovered from Sangala of the bioweapon being tested on innocent people. The President is more resolved than ever to bring down Starkwood. Tim Woods, head of Homeland Security, along with Admiral Smith, bring the President into a secure internet conference with the FBI and Tony. Woods and Smith, upon hearing Seaton's story, concur that they may not get another chance. The President gives Larry authorization to move on Starkwood, and digitally signs Seaton's pardon. Seaton gives the location of the warehouse where the canisters are stored. It will take the FBI ten minutes to reach Starkwood. Renee asks Seaton to get Tony into the warehouse. Jack begs Larry to join them, but Larry can't risk Jack coming down with symptoms while he's in the field. Jack realizes that Larry is right.
Seaton takes Tony to the warehouse and recons via phone with Larry. Inside, Hodges and teams of security and scientists are working on the weapon. They're an hour away from being armed. Larry contacts Starkwood's air tower with an executive order to search that warehouse. Any interference will result in arrest. The air traffic controller lets them in.
Hodges, looking anxious, hears the helicopters approach. Larry has the doors blown open. The FBI team enters to find an empty warehouse. Larry demands to know where the weapons are, and Seaton claims he doesn't know. He says that Tony had threatened to kill him and he only told Tony what he wanted to hear. Larry isn't buying it, but there's nothing to be done but place Seaton under arrest. Hodges observes this scene via a security monitor. He and the weapons are in a completely different warehouse on the other side of the compound. Seaton's bought them some time. Now they just have the keep the FBI over there.
Larry leads the FBI out of the empty warehouse, determined to keep searching Starkwood, but he's met by a heavily-armed team led by Stokes, who is still alive after all. He says they cooperated with the FBI's demand to search this particular warehouse and now asks them to leave. They are on private property. As the groups take aim at one another, Stokes says that Starkwood will defend themselves against a hostile government that is trying to shut them down and will be within their legal rights to do so. If the FBI try to advance any farther, they will be fired upon. Larry doesn't answer. No one moves. No one blinks. It's a standoff.