Callen and Sam are trapped in an armed submarine that terrorists have aimed to hit an aircraft carrier in San Diego. Meanwhile, Hetty defies orders and forgoes her trip to Washington, as the team tries to locate and save Callen and Sam and prevent the terrorist attack.
The NCIS: LA team discovers that one of their own is compromised when they investigate the murder of a Navy contractor involved in illegal transactions of confidential data. Meanwhile, Hetty is under investigation in Washington, D.C., when the Department of Justice arrives in L.A. to investigate the team.
The team takes action to protect one of its own while being interrogated by the Department of Justice. Nell goes undercover. Hetty and Director Vance give Hetty disturbing news while she is in Washington.
When the team learns that someone from its past is targeting one of its own, they desperately search the city. Operational Psychologist, Nate Getz visits Nell to help her through her traumatic experience.
Callen and Sam make their way to Mexico to locate the only employee who escaped a professional hit at the Department of Defense. Back in America, the rest of the team work to discover the motive behind the shooting.
When Sam is arrested for murdering a woman, Callen and Granger work to clear his name. Kensi and Deeks discover a link between the victim and a student from Sam's past.
When a man is murdered by a small drone, the team discovers his connection to a terrorist group that is planning another local attack. With time running short, Nell must use her drone expertise to try to divert a disaster in Long Beach.
Kensi and Deeks investigate the murder of a homeless man, who was a former marine and CIA agent. The probe reveals the victim had connections to the Mexican cartel.
After Granger is poisoned by the mole and Eric is one of the seven suspects, Hetty orders a lockdown while everyone is investigated.
Sam reflects on his own upbringing and relationship with his father when the team investigates the murders of marines who have sons in military academies.
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.
While Callen is undercover in the mail room of an office building to investigate an arms dealer, it is over taken by terrorists and Callen becomes a hostage. When the team arrives to help, they discover the entire building is wired with explosives.
After U.S. Ambassador Nancy Kelly narrowly escapes a terrorist attack at the U.S. Consulate in Tunisia, Callen and Sam are sent on a secret, dangerous mission to obtain key evidence from the crime scene. Upon their return, the team seeks Kelly's help to provide missing information.
Callen and Sam go undercover as food truck owners in Mexico to find the source of an anthrax poisoning before it's used to create a bioweapon.
Callen and Sam are kidnapped when they follow an anonymous tip about a missing NSA agent. When the team discovers they are nowhere to be found, they realize it could have been a trap set by terrorists.
When Callen and Sam are tasked with apprehending a spy contracted by the CIA, Sam is shot and the team enlists the help of Thapa, the elite Nepali soldier from their past, to help to find the shooter. Also, Kensi and Deeks have their first official argument.
While the team investigates the death of one of three Afghanistan soldiers who are training in the U.S., they discover two other soldiers are missing and must find them before they're forced to reveal classified military operations to their captors. Also, Sam is back to work but his team worries it may be too soon, and Callen realizes he has very little in common with his partner.
When three FBI agents are killed in an explosion following a successful undercover sting operation, the team searches for the person behind the attack. Meanwhile, Deeks and Kensi realize the team knows about their relationship, as Hetty pairs Kensi with Sam and Deeks with Callen during the investigation
When a missile test is hijacked and sent off course, the team searches for the hacking group responsible for the attack with the help of a young computer specialist Hetty brings in to assist the team. Also, Nell sees the bond between the tech guru and Eric and she becomes jealous.
Callen and Sam resume their undercover identities as a prisoner and guard to infiltrate a white supremacist group believed to be in possession of stolen nuclear material, while Kensi transforms herself into a tattooed biker to play the part of Callen's girlfriend. Also, Callen's first meeting with Hetty is revealed.
Callen and Sam are shocked when an old acquaintance, who they thought was the recent victim of a murder, appears and asks for their help. As the team investigates, they uncover a possible breach of America's economic sanctions against Russia.
The team searches for a former Marine and expert sniper who escaped a veterans hospital when they discover his connection to the leader of an extremist group. Also, the case reminds Kensi of her past as a sniper.
Callen and Sam search for answers when they find dead crew members from the missing oil tanker used in Arkady's deal with Russia, and also discover Arkady's personal connection to the ship.
The case involving Arkady and his personal connection to an oil tanker now leads Callen, Sam, Deeks and Kensi to Moscow, where the team must assume multiple undercover identities to locate their suspects. Meanwhile, Callen uncovers new information regarding his father, on the sixth season finale.