Curtis tells Audrey that the EMP cut off all connection to Jack and Paul. Although an EMP bomb only affects electrical systems, no one knows if they are safe.
Conlon's guards beat up Paul, who refuses to divulge any information. After Conlon leaves, Jack saves Paul. They find the printouts that Paul hid in another office. Jack takes it and helps Paul escape.
Heller introduces Michelle to the CTU staff as the new director. Tony briefs her on what they have found so far about Marwan and McLennan-Forster. Michelle says that the only priority is to find whatever information Jack uncovered.
Michelle assigns Tony to run a cross check of names, and Tony cannot hide his anger that his abilities are not being put to better use. She blames it on his being an alcoholic the last time she saw him. She says he can resign if he doesn't want to follow her orders. He doesn't, and Michelle bestows him with a low-level security clearance.
Audrey notices this exchange and she warns Michelle that Secretary Heller doesn't like personal problems affecting the job. Michelle becomes defensive.
Curtis and Edgar watch a news report of looting and gunfire in the area near McLennan-Forster. They suspect that the company must have set off the EMP because they were incriminated in whatever Jack uncovered.
Marwan enters his restaurant hideout and calls a man named Mitch Anderson. Anderson assures Marwan that he is ready and that it will take him less than thirty minutes to get where he is going. Marwan confirms that he will inform the others. Anderson pulls out an Air Force uniform from his closet.
On her monitor, Sarah spots a helicopter heading to McLennan-Forster that won't respond to any of CTU's requests. It is not a police or rescue chopper. Tony knows that this means it is a search and destroy mission composed of at least 20 armed men. He suspects that McLennan-Forster sent it to go after Jack and Paul. The company has been training mercenaries for years. Michelle throws a look at Tony for interceding in her authority.
Outside the building, Jack and Paul try to avoid the beam of the chopper as it lands. Conlon comes out with photos of Jack and Paul. He instructs the mercenaries to have the men "erased" even though one of the targets is a federal agent. Conlon says that Jack went bad and started helping the terrorists. They spot two bodies on infrared, and they go after them.
Jack carries Paul through the darkened streets to a sporting goods store in search of weapons. As they approach, a gunshot fires through the front door and a voice warns them to stay back. Jack identifies himself as an agent. Two Arab American brothers are huddled inside. They have just had their store looted.
Jack takes their supply of rifles and explains that he's trying to fight back against the people who set off the EMP bomb. These people were also responsible for the terrorist attacks. Jack urges the brothers to flee. Jack plans to engage the McLennan-Forster army with firepower to force them to use their radios. This will signal CTU. The brothers decide that they want to stay in their store to help Jack because they have been fighting the stereotype of terrorists their whole lives.
Audrey admits to her father that she was shocked to see Jack torture Paul because he seemed like a different person than the man she fell in love with. She says she's not sure if she still feels the same way about him anymore.
Sarah lets Michelle know that Driscoll had promised her a raise after being falsely accused. When Michelle dismisses her, Sarah threatens to go over her head to Heller. Michelle can't afford to have someone she doesn't trust. She calls security to remove Sarah from CTU and strip her of her access card. "You'll be sorry for this," Sarah says as she is escorted out.
As Conlon and his men approach the sporting goods shop, Jack has the store owners prepare to defend themselves.
Curtis voices his concern that the staff is stretched thin and that they need Sarah back. Yet Michelle doesn't trust her. Curtis suggests Tony, and Michelle reluctantly summons Tony to work with Curtis and Edgar.
With Jack and Paul still not located, Tony disagrees with Michelle's call to have the tactical teams surround the perimeter of the EMP blast site. He knows Jack will start a firefight to force the enemy to break radio silence because it's the most efficient way of being found. Despite Tony's plea, Michelle refuses to change the plan.
Jack sees the McLennan-Forster commandos advancing, and he readies his crew with their weapons. Jack fires one shot, deliberately missing a mercenary. Just as Jack suspected, the commando radios his forces for backup. Jack and his team wait.
Michelle apologizes to Audrey for being antagonistic towards her earlier. Audrey thinks she is being too harsh on Tony. She explains that Jack turned to him when he had no other choice, and that Tony saved their lives. Audrey adds that Tony still cares about Michelle.
Michelle approaches Tony and says that she does value his input. "Don't patronize me," Tony laughs. She tells him that, based on his experience, she will consider what he says seriously. Tony snidely remarks that he will always tell her what he thinks.
As they lie in wait, the brothers tell Jack that their father left them the business after he died. They think he would have approved of their fight against the terrorists. Paul thanks Jack for saving his life.
Tony questions Audrey on Jack's sudden change from desk job to field agent. She thinks that Jack will want to return to Washington, but Tony isn't so sure.
Edgar sees radio frequencies being used near the McLennan-Forster headquarters. Curtis acknowledges that Tony was right about Jack's forcing an attack.
The commandos get into position outside the sporting goods store. Conlon gives the orders to move in, and they begin firing. Jack and his cohorts shoot back.
Edgar gets infrared proof that there is automatic gunfire at the spot of the radio transmission. Audrey becomes concerned, and Curtis says that the ground forces won't be there for another 5 or 6 minutes. Michelle looks around, sheepish. She knows that her decision was wrong.
Conlon becomes aware that civilians are helping Jack. He gives the order to get the documents. Jack and his team continue to fire back.
Jack orders his men to retreat into the back of the store. The McLennan-Forster mercenaries blow open the store's entrance and raid the premises. Jack instructs his men to shine their flashlights into the commandos' eyes to counteract the night vision goggles.
Edgar sees that the gunfire has stopped. They suspect that Jack and Paul could have been captured, along with the incriminating evidence they were protecting.
CTU teams get to the location, but they have no verification on Jack and Paul. Tony stresses to the SWAT leader that the hostiles cannot leave the site because there is evidence still at large.
Conlon moves in with his night goggles, and Jack flashes the light on him and shoots him down. Jack doesn't notice that Conlon is still alive.
The SWAT team arrives and they notify CTU that they have taken out all the hostiles.
Tony lets Michelle know that Jack was saved. She offers him the task of decoding the encrypted document, but he suggests that Curtis take over. Michelle apologizes for bringing up his drinking. Tony wants to leave, but she says she can't afford to lose him. He agrees to stay.
Jack thanks the brothers and promises to get them help putting their store back together. He gives the encrypted document to the SWAT leader to send to CTU. Paul sees Conlon rise up and aim his gun at Jack. Paul pushes Jack out of the way, taking the bullet instead. Jack kills Conlon once and for all. Jack tries to keep Paul conscious. "I owed you," Paul says weakly. The medic tries to save him.
Wearing his uniform, Anderson calls Marwan from an Air Force base. "The President of the United States is on a tight schedule," Marwan says. "We can't be late."