Ducky (DAVID McCALLUM) and his assistant Gerald are called in late one night to perform an autopsy. However, as Gerald opens the body bag, a gun-toting man jumps out and holds them hostage. While he won’t tell them his exact motives, he has them pull out the body of recent shooting victim Qassam. Suspected terrorist Qassam had been killed in an incident on the Norfolk base by Gibbs (MARK HARMON), and captor Ari wants all of the evidence linked to him, including his blood. So, as the next morning comes, Ducky gruffly dials up Abby (PAULEY PERRETTE) and asks her to bring all of the evidence that had been sent to forensics. Currently having nightmares about the autopsy room, Abby convinces Kate (SASHA ALEXANDER) to go in her place. But prior to heading down to autopsy, Kate calls Ducky, and soon realizes that the situation downstairs is amiss. Unaware of any of these logistics, Gibbs is continuing the investigation of Qassam, including a search of his apartment to ascertain his terrorist ties.
When Kate arrives at autopsy, she is held hostage too, as Ari realizes that she has a gun. As Ari holds all three of them at gunpoint, Gibbs, Tony (MICHAEL WEATHERLY) and Abby start piecing together that a crisis situation is looming in the autopsy room. Gibbs pulls up a camera view of the room, but only snow flickers on the screen. With that revelation and now calling in the FBI, Gibbs and Tony head to the room above autopsy to insert a lens to get a view of the hostage situation, and how many captors they’re dealing with. As they do, they find one and get his image on screen. The situation is growing dire though as Ari has shot Gerald as a way of scaring Kate and Ducky into cooperating more fully with him. Worse, Ari finds the secret lens Gibbs planted and destroys it.
Meanwhile, Gibbs communicates with NCIS field agents in Bahrain and Gitmo to ascertain more about Qassam and his link to Ari, their terrorist motives, and whether they are Al Qaeda or Hamas operatives. Ari is also now demanding any evidence that has been confiscated from Qassam’s residence. Working with Abby as she delves into that evidence, Gibbs deduces that Qassam was using his work position –as a burger flipper on the Norfolk base – to contaminate the military personnel with a virus. Sifting into Qassam’s personal effects from his apartment, Abby finds a strain of small pox in a sinus inhaler but, fortunately, that strain was not in Qassam long enough to have infected anyone. Before turning over the evidence to Ari, Gibbs arranges for duplicates of all the items so that they can preserve the original evidence. With further help from the NCIS field agents, Gibbs realizes that Qassam and Ari are Hamas operatives and Ari wants all the evidence so that Qassam’s previously covert moves on behalf of Hamas – though unsuccessful – will remain secret.
Upon his evidence demand, Ari has also requested an in-person meeting with an unarmed Gibbs. Eager to end the stand-off and save Ducky, Kate – and a worsening Gerald – Gibbs agrees and heads down to autopsy with the box of duplicate evidence in hand. As he does, SWAT teams have set up posts around the building to thwart any exit Ari will try to make. In the autopsy room, Gibbs and Ari engage in a tense game of one upmanship and – in a gun battle that ensues – Gibbs shoots the terrorist, who also injures him. SWAT teams then swarm in to secure the situation as Gerald, Kate and Ducky are taken to safety.