The episode begins with a guy on a bike wanting to get in the front door of a building, but he is stopped by McGee, who tells him to use the rear entrance. He goes in the back and a homeless man throws trash at him; it’s Gibbs. The man moves on and passes Ziva who is all dolled up and talking on her cell phone. The man gets suspicious of the homeless guy and takes Ziva hostage. Gibbs draws his gun. The man tries to lead Ziva out, but when he passes the dumpster, Tony pops up and grabs him, Ziva punches him and NCIS gets their man and his laptop. This is going to leave a big hole on the Most Wanted list. Back at NCIS, Tony enjoys the capture. They took down Ajay Khan, the guy who hacked into MTAC last month, and he is the No. 2 cyber terrorist, who they hope can lead them to No. 1.
But in the meantime, the network is down. Tony complains to Kevin from IT that they cannot track down the No. 1 without their computers. Kevin explains that there are new security measures in place. Kevin gives Ziva a flier about an Improv comedy night to give to McGee. Because of his beard, he says, he usually ends up playing a bumbling terrorist. In interrogation, Ajay calls his lawyer, who can't make it until tomorrow. Gibbs doesn't care and forces Ajay to look at photos of Agent James Hunt, who was undercover when Ajay's hack took down the system and exposed his position. Ajay tells him that his employer goes by M.C., but he doesn't know where he is. Ajay knows that Gibbs has nothing on him to make him talk.
Gibbs tells Tony he said "UP address" instead of "IP" so Ajay would think they are dumb. In the lab, McGee dismantles Ajay’s laptop and Abby supervises closely. McGee tells her that Ajay too went to MIT and he hacked into the database in his freshman year. He manages to turn on the laptop in a way that his computer won’t know that it is on; let alone be snooping; but the motherboard starts smoking; it is a failure. Duckie explains to Gibbs that Ajay is motivated only by money. He doesn't have any family or friends, because he is narcissistic. Duckie thinks he would worry about losing it all or dying. Khan had double crossed a terrorist group which is now being held in Guantanamo.
In MTAC, Gibbs conferences with Air Force Brigadier General Jack Mandrake to arrange a three hour intimidation trip for Khan to Gitmo. Craig joins Gibbs and balks at Gibbs’ idea. It is very unorthodox and he won’t be able to sell it to higher authorities. Gibbs visits Abby in the lab. She captured some of Khan's computer booting up on camera. She has an address of a warehouse in Anacostia. Tony and Ziva check out the warehouse, which is big, dark and empty. But they do find a dead body; and it is definitely not death by natural causes! Tony asks Ziva to call the Hazmat. Gibbs shows Ajay the picture of the dead man, Robert. He was killed by ebola virus. He was the warehouse caretaker who doubled as a bomb maker. Gibbs mocks him saying that the use of ebola is unoriginal.
Khan says that it was MC’s idea. Gibbs once again mocks him by saying that he is not even the brains of the operation. Gibbs asks McGee to pay up. But Khan tells him that he should wait for 20 days before he does so. Gibbs got what he wanted. McGee walks in with an orange jumpsuit. Next, Khan is shackled and strapped into a transport plane to Guantanamo. Ziva and Tony join him. Khan tells Gibbs he doesn't believe they're going to Guantanamo. But he still refuses to talk. The plane takes off. Gibbs visits Duckie in the morgue. Duckie found a cut on Robert’s finger, which could be how he was given the virus; but he was given a weakened strain of the virus. And this adds to the mystery!
Craig comes to get Gibbs to go over the plan. He's not sure what to do if Khan doesn't start talking before the plane lands. Gibbs tells him that if it comes to that, it will be Craig’s call to make. On the flight, Khan is continuously throwing up. Ziva tells Khan that his former employers, who he double crossed, are at Guantanamo. Khan doesn't think they have the power to arrange to put him in holding with them. Craig visits Abby in the lab. She found the ebola strain was developed as a vaccine by the CDC to help people, but their system was hacked and the vaccine was shipped as a flu vaccine. Craig realizes this means that anyone who opens the boxes for the flu vaccines could unknowingly release ebola, putting hundreds or thousands of lives in danger.
On the flight, Tony talks on the phone about changing the game. Khan does not take them seriously even now. Tony takes out a syringe and injects Khan with something, knocking him out. Kevin nervously looks around for Gibbs with a replacement phone. Abby announces she has tracked the ebola shipment which was shipped to the warehouse. They are now on delivery trucks that have GPS. Craig calls for Kevin. Khan wakes up in a cell with Tony and Ziva looking over him. He hears shouting in Arabic, Ziva translates: "Give him to me, you pig, you coward. Die!" They leave Khan alone in his cell, surrounded by screaming terrorists. Metro PD helps NCIS set up a checkpoint to intercept the delivery truck. In the cell, Khan still refuses to talk. An army guard tells Tony and Ziva the base commander wants to see one of them.
They tried to keep it low profile but looks like the game is over. Khan isn't legally supposed to be there, so one of them has to stay with him. Khan enjoys seeing them busted. The guard leaves Tony a walkie talkie and Ziva leaves with the guard. Back in DC, Gibbs and McGee pull the driver out of the truck. But the driver doesn’t know anything about the samples. In the cell, Tony tries to understand his motivation. Khan says it's about a steady paycheck and power. The cell door opens and Tony notices the guards are gone and the cameras are off. Khan thinks it is all part of the plot, until the lights go out, a security breach alert comes over the loudspeakers and they hear gunfire in the distance.
Tony doesn’t have his gun as he was required to check his gun at the gate as per base protocol and he can't reach anyone on the radio. They hear shouting in the distance. Ziva radios back, telling Tony the entire security system is down. It may have been hacked. Khan thinks his boss found out he was there and might think that he is going to flip. Tony goes to investigate, telling Khan to shut his cell door. A guard walks into the cell block and starts to explain when another prisoner's door opens and he attacks the guard. Tony tries to help but is shot in the leg. Khan hides in his cell and he is petrified. In DC, with the truck enclosed in a Hazmat tent, McGee and Gibbs put on Hazmat suits and find the box with the ebola virus.
It's rigged to blow. Back in Gitmo, the prisoner throws Tony to the ground, gets the guard's gun and shoots him in the leg. The prisoner is about to shoot him when Ziva comes and shoots the prisoner in the back. Tony and Ziva go for cover in Khan's cell as they hear more cell doors open. They only have eight bullets to fend off an angry mob. Back in DC, everyone runs for cover from the ebola bomb. It explodes in the tent, but the team manages to contain the explosion. Gibbs gets a call from Craig. Back in Khan's cell, Tony uses his belt to stop the bleeding. Ziva translates a terrorist banging on the other side of the door, saying he will let Tony and Ziva go if they give him Khan. Tony thinks about it and agrees as Ziva says that Khan has been of no use to them. They are about to open the door and throw Khan out when he agrees to talk.
Ziva holds the cell door shut as it is being banged on from the outside as Khan tells McGee back in DC how he contacts MC. McGee doesn't believe Khan's first answer and cites an old hacking trick Khan used at MIT to make Khan tell the truth. He gives them MC's IP address so McGee can track him. They radio Gibbs that they found MC. The lights come on in the cell, Tony takes the tourniquet off his "hurt" leg and the cell door opens to reveal Gibbs and an unhurt "guard" and "prisoner." Kevin was the terrorist screaming in Arabic; his practice for the Improv comedy. The team leaves the holding facility at Andrews in the blowing snow; they were not in Cuba! The episode ends.