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Season 6 ends with the team traveling to Moscow where they assume multiple undercover identities to locate suspects in an ongoing case. Meanwhile, Callen uncovers new information regarding his father.
Callen and Sam search for Arkady when crew members from the missing oil tanker used in his deal with Russia are found dead in the ocean. Their investigation also uncovers Arkady's personal connection to the ship.
The team search for an expert marine sniper who escaped from a veterans hospital when it's discovered he's connected to the leader of an extremist group. Meanwhile, the case reminds Kensi of her past as a sniper.
Callen and Sam are shocked when an old acquaintance they thought had been murdered shows up and asks for their help. Their investigation uncovers a possible breach of America's economic sanctions against Russia.
Callen and Sam work undercover as a prisoner and guard to infiltrate a white supremacy group believed to be in possession of stolen nuclear material. Kensi transforms herself into a tattooed biker chick to play Callen's girlfriend. Meanwhile, Callen's first meeting with Hetty is revealed.
The team investigate when a missile test is hijacked and the missile is sent off course. Hetty brings in a young computer specialist to assist in the probe, but Nell becomes jealous when the tech guru and Eric start to bond.
The team investigate when three FBI agents are killed in an explosion following a successful undercover sting operation. Meanwhile, Deeks and Kensi realize Hetty knows about their relationship when she pairs Kensi with Sam, and Deeks with Callen during the probe.
The NCIS team must find two missing Afghanistan soldiers who are training in the U.S. so they can't disclose classified military operations to their captors. The team worries that Sam is back to work too soon and Callen figures out that he and Sam have very little in common.
Sam is shot while trying to apprehend a spy contracted by the CIA. The team enlist the help of Thapa, the elite Nepali soldier from their past, to help locate the shooter. Meanwhile, Kensi and Deeks have their first official argument.
Callen and Sam are kidnapped when they follow an anonymous tip about a missing NSA agent. When the team discover they are missing, they realize it may have been a trap set by terrorists.
Callen and Sam work undercover as food truck owners in Mexico to find the source of an anthrax poisoning and prevent a bioterrorism attack.
After the U.S. consulate in Tunisia is attacked, Callen and Sam go on a secret and perilous mission to retrieve key evidence from the crime scene. When they return, they seek help from the U.S. Ambassador, who narrowly escaped the attack, to provide missing information.
Callen is taken hostage when terrorists take control of a building where he is working undercover to investigate an arms dealer. When the NCIS team arrive, they discover the entire building is wired with explosives.
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.