The CTU staff learns that Logan was sworn in as President. Jack calls from the desert after reconstructing the pages missing from the Playbook with the Defense Department. Those pages correspond to nuclear weapons, and some of them are traveling between checkpoints.
Marwan cross-references the coordinates in the Playbook to find one warhead being shipped to Iowa. He and his associate figure out where they can intercept the warhead in transit, and they contact their people to get in place.
Chloe alerts Michelle and Tony that a man named Yosik Khatami just used a credit card at a gas station under an assumed name. Yosik is on a watch list for his affiliation with Marwan. Michelle orders Curtis to head to that location.
Jack calls Audrey from a helicopter as he heads back to CTU. She explains that a lot of the weapons being shipped were to be dismantled, but that many of them were re-routed after the morning's train bombing. Through tears, Audrey admits to Jack that the doctors are having a hard time keeping Paul's condition stable.
Yosik calls Marwan from the road and confesses to making a mistake. He used the wrong credit card when he stopped for gas and now he might be traceable. Marwan instructs Yosik to go to the Marina where someone named Prado can meet him to make arrangements for his escape.
As President Logan heads to the Bunker, Novick tries to convince him that by remaining in the Oval Office he will exhibit a greater sense of confidence. Logan doesn't listen.
Logan seems eased that he will be safe in the Bunker if the White House gets hit. The CTU chiefs call the President with an update on Marwan. Logan is frustrated that CTU has no assurance that Marwan will be caught. He says that he is not going back upstairs until it is safe. Novick interrupts and tells the President to let the CTU team get back to work.
After hanging up, Tony voices his concern about Logan's leadership based on the fear he exhibited in the call. Buchanan gives Logan the benefit of the doubt and suggests they give the man more time to adjust to his new position as President.
Chloe informs the bosses that they have found Yosik's car on the satellite. Buchanan wants Curtis to know who the man is meeting before he picks him up.
Tony apologizes to Michelle for what he said about Buchanan. He asks if they can leave all the tension from the past behind so they can do their jobs.
Michelle asks Tony to stay on the floor while she and Buchanan run tactical with Curtis. Buchanan tells Michelle that he doesn't think Tony can stay focused with the interpersonal dynamics between them. Michelle is confident that Tony will be fine.
Curtis and his team arrive at the Marina and see Yosik waiting alone on the dock. A man approaches. Yosik greets Joe Prado but says that there is someone else there. Yet it is only a local security guard on detail.
Prado takes Yosik onto a boat for privacy. Yosik is terrified that he's been caught. Curtis confirms to CTU that the man who just arrived is not Marwan, and he orders his teams to move in.
Prado looks out from the boat and sees the impending raid. The agents announce that they have surrounded the boat. Yosik calls Marwan to tell him he's been found. Marwan orders Yosik to kill Prado because he knows too much. Yosik reaches for his gun, but Prado kills him. Marwan hears this over the cell. Prado exits the cabin to the throng of agents. Marwan listens as Prado claims he shot the man inside because he was trying to steal the boat. Curtis captures Prado and radios this into CTU. Curtis also has Yosik's cell phone, but Marwan has been disconnected.
Marwan wants to contain Prado so that he doesn't talk to the police. He calls someone and asks them to contact an attorney at Amnesty Global. Marwan wants it reported that an innocent man is being tortured at CTU in Los Angeles.
Everyone at CTU watches the television as Logan addresses the nation. Audrey interrupts with news that one of the convoys headed for Iowa is missing and hasn't called in at its checkpoint. The convoy was carrying a nuclear warhead.
Edgar gets Prado's photo and fingerprints from Curtis for a background check. Michelle has the rest of the staff focus on finding the warhead. After learning about the missing nuke, Novick complains to Buchanan that the President won't be happy that the statement he just made has become invalidated.
At the site of the torched, ambushed convoy, a group of men put the crated warhead onto their flatbed truck and throw a tarp over it. They drive off.
Logan questions Novick about the missing warhead, and he becomes agitated when there are no answers about stopping Marwan. Logan suggests that he is the next target. Novick remains calm.
Curtis and the agents lead Prado into CTU. Edgar makes a comment to Chloe that he'd like to get Prado in a room alone. Chloe dismisses this bravado as his desire for revenge for his mother's death. Meanwhile, Tony briefs Curtis that Prado is an ex-Marine who has no record of employment for the last five years. Prado must be a criminal or mercenary.
Chloe gets word that the Iowa highway patrol discovered the convoy that was ambushed. The drivers are dead and the warhead is gone. Tony has her find out what kind of vehicle could transport the nuke. She will also set up perimeters and check for local airstrips.
Michelle warns Curtis that Prado is a Marine who won't cave easily. Curtis wants to use Richards, the torture specialist.
Prado tells Curtis he's got nothing to say. Yet Prado is shocked when Richards unsheathes his torture needles. Suddenly, Michelle gets a call from Buchanan to halt the interrogation. She asks Curtis to step out.
Michelle and Curtis meet with Buchanan who is accompanied by a lawyer from Amnesty Global. The attorney has a signed court order protecting Prado. Buchanan tells Curtis to take the lawyer to see Prado while he calls the Justice Department for help.
Edgar is furious that Prado is getting off because of some lawyer when his mother had to die for no reason. Buchanan urges Edgar to put his emotions aside and get back to work.
After Edgar leaves Buchanan's office, Chloe pushes Edgar to focus on doing his hourly reports.
Jack enters CTU and Chloe tells him that a lawyer got the interrogation on Prado suspended. Ignited with anger, Jack goes to Buchanan, who explains that the Judge thinks that Prado cannot be held because he is not a known terrorist. Jack is furious and goes to leave. Buchanan warns Jack not to make it worse.
Jack enters the interrogation room and pulls the attorney aside. He points out that millions of lives are at stake, but the lawyer won't budge. Jack asks how he found out about the prisoner so quickly. The attorney refuses to say who told him about the arrest.
Curtis confirms that Prado would have had no time to call anyone. Buchanan notes that Marwan could be involved. Jack says they need to contact the President.
Logan and Novick take the call from CTU. Buchanan explains that the prime suspect cannot be questioned because of Amnesty Global's interceding. Logan can't grasp what CTU is asking for, and Novick interjects with the assumption that the questioning needs to be done behind closed doors.
Logan surveys his aides. Novick wants to let CTU do whatever is necessary, but Walt Cummings is worried that this will taint Logan's Presidency. Logan compromises by calling for a special session of the Justice Department, He tells CTU that it will take at least twenty minutes. Jack begs for the chance to do their jobs properly without intervention, but Logan says he will get back to them as soon as he can.
Jack asks Buchanan to make a judgment call without the President. Jack wants to resign and let Prado go free. He plans to take him on as a private citizen, and then no agency will be held liable.
Marwan speaks to the driver of the truck holding the nuclear warhead. The man the truck is to meet will have the bomb's detonation codes. Marwan does not want to give the Americans time to start evacuations. Marwan hangs up. He is near downtown Los Angeles.
Audrey comes upon Jack, who hurriedly packs up a taser gun. Jack walks away from her in a rush and refuses to answer where he is going.
Tony and Curtis let Prado out of custody. Although Prado is suspicious, his lawyer assures him that CTU knew their backs were against the wall. Fearing for his life, Prado refuses to leave. Curtis threatens to arrest him for trespassing on a government building.
Edgar is incensed that Prado is being released. Buchanan won't give him answers.
Outside CTU, the lawyer leaves Prado and tells him he will be fine. A U.S. Marshall accompanies Prado to a government car.
After the attorney pulls out of the lot, Jack tasers the Marshall and slaps handcuffs on Prado."Now we're gonna talk,"Jack says as he slams the door of the car.
When Prado claims that he doesn't know Marwan, Jack breaks the man's fingers one by one. Prado finally relents, and confesses that Marwan will be at a place just east of downtown."This will help you with the pain,"Jack says as he knocks Prado out with a punch.