The NCIS team's LAPD liaison officer, Detective Marty Deeks, goes missing while undercover, right after the subject of his investigation is killed by a bomb planted in their car. LAPD Detective Jess Traynor, Deeks's partner, dies from a similar car bomb just after briefing NCIS. The team is tasked to find the missing detective.

An NCIS undercover agent is assassinated while in Cyprus investigating illegal arms sales to Chechen extremists. The same hit team is later detected arriving in Los Angeles, and the NCIS Los Angeles team is in a race against the clock to stop the assassins from killing their next target, a suburban housewife who is more than she appears to be.

Four marines are ambushed while participating in a joint DEA-Marine task force interdicting Mexican criminals along the U.S.-Mexico border. The NCIS team works to recover the captured marines and uncover the mastermind behind the operation: a textile manufacturer that wants the US military to go to war with the cartels so they will stop interfering in his factories south of the border.

The NCIS team investigates the murder of a sailor with top-level security clearance after he is found dead and missing a hand in a Rodeo Drive parking lot. The case takes a turn after it is discovered he was selling artifacts that were looted from a museum during his tour in Iraq.

When the teenaged daughter of a Navy commander is kidnapped by what appears to be a serial killer who buries his victims alive, the team needs to determine whether he is the target of blackmail for military secrets or if the crime is random. Sam takes the case personally after getting flashbacks of being buried alive while doing a mission in Bosnia as a Navy SEAL.

After a downtown Navy Recruitment Center is held hostage by Callen's ex-CIA partner and undercover wife, Tracy Keller (Marisol Nichols), he realises she is searching for him for help. Tracy explains she is on the verge of exposing a group of corrupt FBI Agents and their arms dealer contact in the aim of recovering stolen missiles. But not everything is as it seems, and the NCIS team worry whether Callen has fallen under the charms of his ex-wife.

A State Department employee and plastic surgeon are murdered. The team discovers a terrorist cell has had their faces surgically altered. They must find the one person who can identify them and foil an impending terrorist attack.

The team investigates the murder of a retired Delta Force operator who previously worked with a Marine SOCOM unit tasked to capture high-priority targets in Afghanistan.

The murder of an arms dealer has Hetty and the NCIS team searching for his missing book of top-secret information. The episode ends with Hetty discovering that her "husband", Branston Cole, a security guard, and a nurse have all been killed.

In the aftermath of Cole's death, Hetty and the NCIS team continue to search for a book that was the target of various intelligence agencies, both foreign and domestic. Things heat up when various spies and agencies from numerous countries begin heading to Los Angeles, forcing the team to race against time to stop the respective gangs from tearing LA apart in their search for the book. The conclusion of a two-part episode.

When two men are killed in a shootout, the NCIS team must rely on a former Navy intelligence officer suffering from PTSD to help them solve the case.

The NCIS team uncovers an experimental Navy tracking system when a body containing a top-secret residue is stolen from an autopsy room. It is discovered that the thieves merely needed the eyes of the victim in order to access a locked hospital storage room in order to steal radioactive material. Meanwhile, Callen challenges Hetty on the rock wall.

The NCIS team sets out to find the individual responsible for stealing a classified Pentagon document before the file's decryption code is cracked by the wrong party.

As G goes off the grid for a day for personal reasons, Sam goes undercover in prison in an attempt to infiltrate a Yemen-based terrorist group by getting close to its leader, another inmate.

What begins as a break-in at G's house leads to a pursuit of black market microchips, and a series of double-crosses. Callen agrees to investigate an Indian "slum dog millionaire" who happens to be Arkady Kolcheck's business rival. Kolcheck also promises Callen to shed some light on the cemetery incident (season 1 finale "Callen, G").

Callen and Sam go undercover with the California Highway Patrol to investigate a corrupt group of CHiPs officers and their connection to missing weapons. But a routine job takes a dramatic turn, and a stolen nuclear warhead sends the OSP team scrambling to recover the bomb.

LAPD–NCIS Liaison Detective Marty Deeks's routine is thrown when he interrupts a convenience-store robbery and is shot, but the NCIS team finds out Deeks was targeted, but not to kill him, instead to lure out NCIS Junior Special Agent Kensi Blye by Vakar (first mentioned in "Black Widow").

The story arc that started in the episode "Lockup" is concluded as Sam is sent on an undercover mission to Yemen. But the stakes are raised when it's revealed that the terrorist group has taken a young seven-year-old boy hostage and things get even worse for the team when it's discovered Nate's cover has been compromised which means that Sam has been exposed as well, forcing Callen, Sam and Nate into a fight for survival against terrorists who want them dead.

It's a race against time as the team attempts to foil an assassination plot against a Venezuelan politician on U.S. soil.

A secure facility on a marine base becomes compromised, causing Kensi to go undercover as a thief in the hope of finding out what a world-class thief planned to steal from the secure facility without having her cover blown.

After a rocket engine expert is killed, OSP tech operator Eric Beale goes undercover for the first time to ensure that the classified technology used to build satellites is safe.

To protect his best friend and primary informant from a group of arms traffickers, Deeks must go deep undercover to an old alias.

The stolen canisters from "Overwatch" resurface after a Navy SEAL imposter is set ablaze. Hetty sets her affairs in order as she prepares to resign from NCIS.

Hetty's resignation from NCIS prompts Callen and the team to initiate an investigation to find her. It is revealed that she has been working on a case involving Callen's mysterious past, and that she herself is a member of the family that has been trying to kill him for years.