Kim and Michelle are both worried when they learn that gunshots were fired at the mall. Then Jack calls to give Michelle the news that Tony's been hit in the neck. She is now in command of CTU, but Jack says that if she wants to be by her husband's side, she must turn over her command to someone else. As she's about to leave for the hospital, Michelle is asked to deal with a second Salazar phone call. She orders Kim to be on the lookout for news about Tony while she attends to the investigation.
Michelle and her team listen to the second phone call with instructions for releasing Salazar. Unbeknownst to the CTU workers, it is Gael's filtered voice on the message. Whoever is sending these messages is controlling Kyle Singer's movements and they only have two hours to find him.
Linda calls Kyle from the mall parking lot. She can't get through because security is barricading the entrance. He has her meet him at another location nearby. Meanwhile, Gomez gets in a pickup truck and follows Kyle. Kyle sees Linda's car and makes her slide into the passenger seat while he drives.
Chase approaches Kim in the CTU bullpen to ask about Tony. As she sees Michelle trying to work through her anguish, Kim notes that this must be the reason why Jack doesn't want her and Chase together. Chase wants to interrogate Salazar again, even though Jack thinks it's a waste of time. Kim suggests he run it by Michelle. Chase leaves without doing so.
A doctor from the hospital calls Michelle to get her verbal agreement to operate on Tony. She asks him to call her at CTU when Tony's out of surgery.
Palmer is uneasy about the decision to give in to Anne's ex-husband's blackmail. Wayne tries to convince him that it's the best solution for everyone, including Anne. Their conversation is interrupted by a call from Jack. Jack informs the President that he will be unable to find Kyle Singer before the virus is to be released. Based on the nation's policy, Palmer is unwilling to negotiate with terrorists. He will keep Salazar in prison, regardless of the threat to the lives of American citizens. Palmer hangs up and asks Wayne to arrange a full briefing on quarantine and evacuation procedures.
As they drive, Kyle admits to Linda that he isn't sure that what he got from Mexico is drugs. Authorities have told his parents that he was used to bring some kind of disease into the country, and that it might still be in his body. Linda has him pull over so she can get out. She is afraid of contracting whatever disease Kyle may have. She gives him her father's stolen money. Suddenly, Gomez and his driver pull up. Kyle tells Linda to run away, but the men capture both of them.
Michelle maps out the investigation for the President and his advisors. Dr. Duncan remarks that, with a quick quarantine, she may be able to reduce casualties under 90,000 people. This news is still grim. Wayne tells Palmer that he has a call from Jack.
Jack presents for the President another option that will allow him to preserve the nation's policy of non-negotiation with terrorists while still stopping a virus outbreak. Jack wants to remove Salazar so that it looks like a prison break. From within CTU, it would appear that Jack has switched sides. Yet Jack needs Palmer's approval, even though it means that this will become his last mission and he will become a fugitive from the law. "If you don't say anything, Mr. President, I will accept that as a go for this mission," Jack says. Palmer is silent.
Anne spots Wayne secretly taking a briefcase from an aide, and she asks him where he is going. Wayne says he is attending to government business. She questions whether this has something to do with her ex-husband. Wayne reiterates that it is government business.
Michelle calls the hospital and inquires about her husband. She is told that Tony is still in surgery. Chloe comes in and apologizes to Michelle about pushing work on her because she didn't know about Tony. Chloe then warns Gael about being sensitive to Michelle's state of mind. When Gael's cell phone rings, Chloe asks why he has a personal cell phone on the premises. CTU employees are prohibited from using one because they can not be monitored. Gael dismisses her with a fake reason.
The caller to Gael is Hector Salazar. Hector is frustrated because the American government has not yet agreed to release his brother from prison. After he hangs up, Hector realizes that a gun case on his desk has been opened and one weapon is missing. He draws his own gun, only to find Sergio, Claudia's eleven year-old brother, harmlessly playing with it. Hector teaches the boy how to fire at a target, and Claudia storms in angrily. She takes the gun away and aims it at Hector. Claudia puts the gun down without shooting him.
Kyle and Linda are brought to a warehouse and are locked inside an airproof chamber. They watch as men wearing Hazmat suits spray down Gomez and his driver to rid them of any toxins.
Anne asks Palmer if he is paying off her ex-husband, Ted. He admits that he was forced to do so, but only to protect her. "I can defend myself," she says simply.
Palmer phones Wayne, who is waiting for Ted Packard in a parking garage with the briefcase full of money. The President orders Wayne to walk away from the deal. Ted approaches Wayne's car, but Wayne drives past him without a word.
Gael, Chloe and Adam tell Michelle they can take over her work if she needs to be at the hospital with Tony. Yet there's no way Michelle can leave. Gael offers to take over the Director position for her, and Michelle turns him down.
Jack calls Kim and asks her to generate a prisoner transfer document. She questions this, but Jack says that he is moving Salazar under high security clearance. Jack walks her through the process and she forwards the document to the prison warden. Jack apologizes for their earlier talk. He says that, although he feels overly protective of her after what's gone on in their lives, he trusts her judgment. Jack asks to speak to Chase, and Kim says that Chase went to interrogate Salazar at the prison. Jack hangs up and curses Chase under his breath.
Jack phones Chase, who has just arrived at the prison. He demands his underling return to CTU. "You're in no condition to give me orders," Chase says. He is through with covering up Jack's drug addiction from Kim and everyone at CTU. With that, Chase hangs up.
Chase asks to meet with Salazar. He has to tell the warden that Salazar is behind a terrorist threat before he is allowed in. Chase requests that the security cameras be turned off in the cell. He wraps a towel over his right hand and slams his left fingers into Salazar's throat before punching him. Salazar is stunned by the ferocity of Chase's attack.
As Chase tries to beat the whereabouts of Kyle Singer out of Salazar, Jack arrives. Jack says that he is left with no other options and will need the information out of Salazar as Chase suggested. Chase is surprised by Jack's change of heart, and attempts to apologize for what he said earlier. Jack then knocks him from behind and renders him unconscious in a chokehold. Salazar watches, confused. Jack informs Salazar that he will be walking free. He has Salazar help him drag Chase into the cell so that he can tie him up.
Wayne blames Anne for the potential loss of the election, but she trusts Palmer's actions. She believes that Wayne doesn't want his brother distracted by her. Wayne warns her that he won't stand by while she jeopardizes Palmer's career.
Jack walks Salazar out of the prison and is stopped by the warden, who says that Jack's transfer access codes have expired. Jack blames it on an administration screw-up. The warden lets him through.
Chase bloodies his wrists as he tries saw off the ties. The warden turns the surveillance cameras back on and sees that they are turned away from the cell. He goes down there and finds Chase, bound and gagged. Chase says that Jack has been lying. Meanwhile, Jack is taking Salazar out of the jail when the alarm goes off. Jack punches out a guard and runs out with Salazar. He then forces another guard at gunpoint to open up all the cells electronically. The prisoners are freed in the main hallways, causing havoc in the jail. Chase is handed a shotgun along with the other guards in pursuit of Jack. Jack and Salazar hide.