Black Budget – 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 3rd Choir – The team learns that someone from their past is targeting one of their own. Nate Getz attempts to help Nell get through a traumatic experience.
Praesidium – 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.
Inelegant Heart – 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.
Deep Trouble, Part II – Season 6 begins with Callen and Sam becoming trapped in an armed submarine that terrorists aim at an aircraft carrier in San Diego. Meanwhile, Hetty defies orders and forgoes a trip to Washington, D.C., to help locate Callen and Sam, and prevent the attack from being carried out.
Deep Trouble – Season 5 ends with the team learning that a cartel plans to transport billions of dollars worth of cocaine from Colombia to the U.S. using a submarine. Callen and Sam are assigned the task of locating the missing vessel. Meanwhile, Hetty is called to Washington in response to the mission in Afghanistan.
Exposure – A deadly explosion at a military-sponsored charity event is investigated, as is a news reporter’s claim of who is responsible.
One More Chance – A 10-year-old girl Sam once provided protection detail for in Saudi Arabia goes missing, and he’s convinced her disappearance is directly connected to the theft of software for a new unmanned-aerial vehicle being developed by her engineer father.
Three Hearts – An undercover NCIS agent is taken into custody when he is suspected of working for the smuggler he is supposed to be investigating. Meanwhile, Kensi and Deeks discuss their relationship when Kensi returns to the field.
Windfall – Nell joins Deeks in the field to investigate a case involving a former marine who is being hunted by members of Al Qaeda for embezzling money from Iraq. Meanwhile, Eric is assigned a new partner in Ops.