Jack calls Tony with news that the President called off the air strikes. Tony spots something that tells him why -- a fuel truck pumping RP-7, which is used for surface-to-surface missiles. Hodges must be threatening to launch. Tony's got three charges of C-4 and a remote detonator. Jack tells him to get into the depot and blow those tanks.
Jack calls President Taylor to ask permission. She has been fending off the Joint Chiefs and trying to keep the situation a secret, so she refuses to authorize the plan. Yet the President tells Jack she expects he will do what he thinks is right. Jack takes that as a request to undertake a covert action that she can deny authorizing if those missiles are launched.
Hodges, with Seaton in tow, arrives at the White House for his meeting with the President. Larry gives his stamp of approval to Jack's plan. He will move in as soon as Tony takes out the missiles. Stokes is in charge of the fueling truck, and Tony forces him at gunpoint to lead him to the fuel tanks, where Tony begins setting up the C-4.
Hodges sits down with the President in the Oval Office -- a place he used to be welcome at under the old administration. He wants Starkwood to be involved in shaping her military policy and operations, making them essentially a fifth branch of the military. Seaton hands her a non-negotiable outline of the protocols under which their "partnership" would function.
Tony returns to the fuel truck with Stokes in tow and is ambushed from behind. The detonator drops into a drainage gate. A vicious hand-to-hand fight ensues, and Tony manages to subdue both attackers, but not before Stokes sounds an alarm. The detonator seems to be just out of Tony's reach. Below, Chapman sees the alarm and prepares to launch, but the lead technician wants to be sure it's not a false alarm before he enters the code. Chapman says this is not protocol. The technician refuses to proceed, so Chapman throws him out of the way and does it himself.
Above, Tony sees the launch portal opening. He gropes for the detonator again, and finally gets a hold of it. He presses the button and there is a tremendous explosion. The entire chamber and the men below are vaporized in the back blast. Tony flees the scene.
Larry sees the explosion from a distance and gives the order to move in. Back in the Oval Office, Tim Woods interrupts the meeting to alert the President that the bioweapons have been destroyed. She immediately has Hodges and Seaton arrested. Hodges says she is making a mistake because this doesn't end with him. He is merely a cog in a much bigger machine. She questions what he's talking about. "You'll find out," he says mysteriously as he is led away.
The President calls Jack, who asks for clemency for Tony when he's put on trial. Midway through his plea, he suddenly falls silent. He couldn't remember what he was just saying. The President excuses him, and promises she will take Tony's actions today into account.
Larry locks down Starkwood and recovers Tony, reluctantly taking him into custody. Back at the FBI, Dr. Mercer tells Jack that memory loss is a symptom of the disease. She can't do anything to stop it and it may cause personality changes and hallucinations.
Renee meets with Kim Bauer. When Jack finds Renee, he tells her that he needs to go on record about the events of the day as soon as possible. She informs him that his daughter is in the building and this enrages Jack because he specifically told her not to bring Kim into this. He had accepted dying until Renee put in front of him the one person he has that's worth living for. Renee says that nobody dragged Kim into this -- she has been trying to see him all day and leaving messages with the FBI to reach him. Renee only just got the messages. Kim was at his Senate hearing, but Jack was pulled out before she could get to him. She offers to tell Kim that Jack's not there. Chastened, Jack asks Renee to take him to see his daughter.
Jack apologizes to Kim, explaining that he thought he was doing the right thing by staying away. He encounters so many enemies in his line of work, and that puts the ones he loves in danger. The experimental treatment for his exposure to the bioweapon involves a risk to her if she helps. The slight chance of recovery isn't worth the pain of having her watch him dying. Kim says she doesn't want to lose her father, and the two embrace, sobbing. Suddenly, Jack suffers from a spasm. He tells her gently that it's time for her to go. "I love you so much," Kim says as he leaves.
At Starkwood, an FBI agent is killed by Galvez, a Starkwood commando. He is caught by the agent's partner, who makes Galvez drop the duffel bag he is carrying. Keeping his gun trained on Galvez, the agent opens the bag to find a canister of the bioweapon. He calls Larry to report this, but Galvez overpowers him and shoots him. Galvez then steals the agent's vehicle. Larry sends out the word that a Starkwood commando has the bioweapon and may be escaping in an FBI vehicle. There is enough bioweapon in that canister to take out a small city.
Roadblocks are set up as Larry takes off in a chopper, accompanied by Tony. Janis tracks the GPS of the stolen vehicle. Larry catches up to Galvez, who is now on foot. With no time to wait for backup, Larry has the chopper land. As soon as it does, the helicopter pilot is shot dead. Automatic gunfire strafes their position. Larry and Tony take cover. Tony is unarmed. Galvez manages to shoot Larry in the abdomen. Larry collapses, and Tony scrambles over to check his condition. Larry sees Galvez sneaking up behind Tony, his rifle at the ready. Gasping and barely able to speak, he just barely manages to alert Tony to look behind him. Tony sees Galvez and silently gestures to him. Galvez, unexpectedly, lowers his weapon, deferring to Tony. "I'm sorry, Larry," Tony says as he puts his hands over Larry's nose and mouth to suffocate him to death. Galvez shows the canister to Tony, who has him go find a place to hide it. As Galvez takes off, Tony waits for the arrival of the FBI to come rescue him.