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.

Both Alex and Jada, from Sudan in a previous episode, have reappeared in Los Angeles; while two NCIS agents (on a protective detail) escort Jada to an office in preparation for her giving a deposition, a masked man in an SUV attacks the trio in their car and escapes without injuring anyone. Kensi and Deeks get a name from Jada, then check a warehouse and catch a bad guy; Alex and his family disappear; Sam offers to play water games; Nell finds Alex, then the foursome chat with him; his behavior perplexes everyone; Kensi and Deeks visit an international business firm, from which they acquire important data; Alex finds the gang, surprises them, and chats them up, then they all pitch in and change their plans. Alex calls the main middleman and proposes a deal, which blows up; Alex gets his family back, and the gang keep Jada but lose the middleman, although another agency catches him later.

The team searches for Jada (Ella Thomas), the woman Sam led to asylum in the United States four years ago, after she goes missing. Also, Kensi goes undercover with DEA Agent Talia Del Campo (Mercedes Mason).

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.

Sam receives a distress code from his son that his school has been taken over by a group of extremists, so the team heads to San Francisco to save the hostages.

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.

Sam Hanna goes rogue from the NCIS team in an attempt to stop Tahir Khaled from ever targeting his family again.