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A burglary occurs at a cyber-security company, but Callen is forced to steer clear of the investigation when Hetty tells him that his girlfriend, Joelle, is one of the lead witnesses. Meanwhile, the team discuss their personal holiday travel plans.
Sam reflects on his relationship with his father when the team investigate the murders of marines who have sons in military academies.
Hetty orders a lockdown and Eric becomes one of seven suspects after Granger is poisoned by the mole.
When a former Marine turned homeless is murdered, Kensi and Deeks go undercover for the investigation and find a link to the Mexican cartel.
A man is murdered by a small drone, and the investigation reveals he was connected to a terrorist group that is planning an attack on Long Beach. With time running out, Nell uses her drone expertise to try to prevent a disaster.
Sam is arrested for murdering a woman, but Callen and Granger work to clear his name. Meanwhile, Kensi and Deeks discover a link between the victim and a student from Sam's past.
Callen and Sam travel to Mexico to track down the only employee who escaped a professional hit at the Department of Defense. Back in the States, the rest of the NCIS team work to uncover the motive behind the shooting.
The team members desperately search the city when they learn that someone from their past is targeting one of their own. Meanwhile, operational psychologist Nate Getz visits Nell to help her through a traumatic experience.
Hetty receives some shocking news from NCIS director Leon Vance while she is investigated by the Department of Justice in Washington, D.C. Meanwhile, Nell goes undercover as Hetty to protect a fellow team member.
The team discover that one of their own is compromised when they investigate the murder of a Navy contractor who was involved in illegal transactions involving confidential data. Meanwhile, Hetty is placed under investigation in Washington, D.C., and representatives from the Department of Justice arrive in Los Angeles to investigate the team.moreless
Continuing from last season's finale, Season 6 opens with Callen and Sam trapped in a terrorist's armed submarine headed for an aircraft carrier in San Diego. Hetty ignores her orders to report to Washington as the team tries to locate and stop the armed submarine.