The CIA loses contact with Sam in Sudan with a CIA task force; two CIA agents die, as does a third one; G goes to Khartoum and lends a hand; the gang in LA help, and they find and deal with a mole; G and Sam return to LA and take a friend.

After the decryption of a list of names, NCIS agents continue the search for both Sidorov, a Russian illegal-arms dealer, and leftover Russian sleeper agents with access to surreptitious nuclear bombs; NCIS teams execute concurrent arrests in seven cities around the USA; however, all seven teams find their targets already dead. G and Sam confer with Arkady; afterward G and Sam meet a tail, which consists of three CIA agents, one of whom, Snyder, Sam knows and dislikes; Kensi, Deeks, and others uncover an empty but radioactive secret room; Eric and Nell find Sidorov; Granger gives an order, but Sam pursues another idea, and Granger catches the team, yet he goes their way; the team watch Sidorov; Sam goes undercover, then he and his wife meet with Sidorov; Snyder allows Sidorov to leave the country (without bombs), but he expects him to return; Sam and Snyder walk into the surf at Santa Monica Bay, where the two of them discuss a disagreement.

Hetty, suspecting that Kensi has become a prisoner of Taliban insurgents, sends G, Sam, and Deeks to aid her; G, Sam, and Granger overcome trouble and find Kensi and another; Deeks produces help; all works out; the gang prepare to go home.

The team investigates a burglary at a cyber-security company, but Callen must steer clear of the crime scene after Hetty reveals his girlfriend, Joelle, is one of the lead witnesses. Also, the team discusses their personal holiday travel plans. Kensi and Deeks are given the chance to get even closer to each other.

The team searches for Sam's former partner, Ruiz (Anthony Ruivivar), who disappears while buying a deadly explosive during an undercover operation.

After extensive surveillance footage of Sam's family is found in Africa, Sam and Callen fly there to determine who is responsible and for what purpose. Also, Sam's family is moved from their home to a safe house. Ella Thomas guest stars.

After Sam's wife, Michelle (Aunjanue Ellis), is taken from her home, the kidnappers demand the prison release of Tahir Khaled (Anslem Richardson), Sam's arch nemesis, in exchange for information on her whereabouts.