A lance corporal in the Marine Corps Reserve dies of garroting; he was an informant about the theft of six missiles from the Marine Corps Base; while investigating, G and Sam go undercover; with help they get the bad guys and the missiles.

Callen and Sam go undercover as motorcycle cops to investigate corruption within the force. When their contact is murdered they take on a job in hopes of catching his killer.

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.

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.

While Eric and a buddy, Ira, play an online game, a sniper opens fire on Ira's pad, and thugs break in; the G team look into security involving Russia and Chechnyan separatists; the team safely work out everything. Kensi remains in trouble.

Kensi and Deeks go undercover as cult members to rescue a former Department of Defense employee brainwashed into revealing classified information, as the rest of the team works to prevent the cult from selling the government secrets.

Hetty goes rogue and an agent is kidnapped by the mole.

After a retirement home resident is kidnapped, the NCIS team uncovers a pair of con artists: Ginger and Edward O'Boyle, who hop from home to home scamming the elderly out of their money. Also, Callen confronts his father on his illegal activity and the danger it places on their family.