The body of a Marine leads Gibbs and McGee to the NCIS (Office of Special Projects) OSP division in Los Angeles, where a murder investigation quickly climbs to a matter of national security in which the two offices must work together to resolve.
Meanwhile, Tony begins to snoop into Ziva's personal life.
With the appearance of Mossad agent Michael Rivkin, Tony is forced to question Ziva’s loyalty to NCIS.
Meanwhile, in Los Angeles, Special Agent Callen goes undercover to try to catch a terrorist cell while OSP psychologist Nate Getz discovers the startling truth about Gibbs and Special Agent Lara Macy’s relationship.
Newly located in a Los Angeles mission, the NCIS Office of Special Projects (OSP) welcomes Callen back to the team and races to solve a kidnapping case.
A case involving the murder of a drug dealer turns personal for Special Agent Sam Hanna when he discovers his former Navy Seal comrades are involved.
The team is assigned to track down a missing unmanned aerial vehicle (UAV) after it is compromised during a training exercise killing a marine before it disappears.
The NCIS team searches Los Angeles for the lead suspect of a murdered Iraqi businessman, a former Marine who had been hired by a private security firm to protect him
When a United States citizen of North Korean descent is murdered, the secrets to classified software are thought to be lost until NCIS uncovers a suspect from Director Vance's past.
The NCIS team must find a motive when they discover the body of a marine who had been living a double life as a wealthy bachelor.
Following the murder of a Russian woman, the NCIS team uncovers evidence that answers who and why Callen was shot six months ago.
While Hetty is attending a Senate hearing in D.C., the investigation of a murdered Marine Lance Corporal leads the NCIS team to stolen anti-tank missiles and a dangerous militia group.
Forensic scientist Abby Sciuto joins the Los Angeles NCIS team when a murder case resembles the pattern for a serial killer she has been tracking.
As the courtyard is being transformed with holiday decorations, the NCIS team races to solve the murder of a Marine by an exploding cell phone and to find the remaining men of his former EOD (explosive ordnance disposal) unit before another deadly explosion kills someone else.
The death of a Petty Officer leads the NCIS team to a teenager in Sam's life.
Meanwhile, Hetty is concerned about the effect that the workload is having on the team.
The murder of a recently released convict forces Callen to go undercover solo as an old alias, while Sam and the LA team track him from a distance.
The team rushes to a crime scene after receiving an "agent needs assistance" page and learns that one of their own is in peril.
A crime scene poses a national security risk when the LA team discovers the location was used to create a deadly toxin which is now missing.
While opening a safety deposit box at a local bank, NCIS Special Agent Kensi Blye is shot after three armed assailants enter and hold everyone in the building hostage.
The death of a lieutenant commander appears to be suicide but the NCIS team uncovers evidence corresponding to murder.
Also, Operational Psychologist Nate Getz joins Special Agent Kensi Blye in the field.
After a sailor is killed during an underground street race, the NCIS team determines that his car had been sabotaged and contained confidential Navy equipment.
Meanwhile, Callen is forced to take traffic school.
The investigation of a drive-by shooting has the NCIS team searching Los Angeles for the dead marine's younger brother who may be the next target and the one with the answers.
When an undercover operation has the NCIS team investigating a MMA gym and its fighters, Sam Hanna is tasked with donning gloves and entering the cage for a one-on-one fight.
NCIS investigates the murder of a Navy officer entangled in the world of Hollywood glitz and glamour as the team is joined at Hetty's request by LAPD liaison Marty Deeks.
The NCIS team races to save one of their own when they receive video evidence of Special Agent Dominic Vail being held hostage months after he was kidnapped.
The NCIS team is on the hunt for a terrorist who escaped Army custody during a secretive transfer in Los Angeles.
After Callen's cover is blown and compromises the unit, the NCIS team races to find out who is behind the security breach.
Callen races against a ruthless adversary to locate a woman who knows the whereabouts of a forgotten fortune earmarked to fund a new war in the Middle East - and also holds the tantalizing key to his unknown past.
When one of their own disappears while undercover, the team must work alongside LAPD on a case involving human-trafficking, money laundering and drugs.
After a mysterious hit squad takes out a Special Agent on assignment, the NCIS team jumps into action before the next target is set.
The NCIS team jumps into action when video surveillance footage shows an ambush on a humvee transporting Marines in the desert. Meanwhile, Nate returns from his mystery assignment.
The NCIS team investigates the murder of a Marine with top-level security clearance after he is found dead and missing a hand in a Beverly Hills parking lot off Rodeo Drive.
A videotape revealing a Naval Commander's daughter being buried alive strikes a nerve with Special Agent Sam Hanna and thrusts the NCIS team in a race against the clock to save the girl before time runs out
After a downtown Navy Recruitment Center is held hostage, Callen mediates with his ex-partner, Tracy Keller, to uncover information about a hijacked shipment of Spike missiles.
After a state department employee and a plastic surgeon are murdered by a group of terrorists, the NCIS team must frantically search for the only witness who can identify the killers
When a former Army Sergeant responsible for hunting down high-value targets is found dead, the NCIS team searches for terrorist leaders suspected of his murder. Meanwhile, Deeks bonds with a person of interest in the case, making him more determined than ever to track down the killers.
A murdered antiques dealer has Hetty and the NCIS team searching for his missing book containing top-secret information in part one of a two-part episode.
Hetty and the NCIS team continue to search for an elusive book that has the attention of several foreign security agencies.
Kensi connects personally with a discharged Navy Intelligence officer suffering from post traumatic stress disorder who is the sole survivor of a deadly dispute being investigated by the NCIS team.
The NCIS team uncovers an experimental Navy tracking system when a body containing a top-secret residue is stolen from an autopsy room. 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.
Sam goes undercover as a prisoner to track down a terrorist group responsible for several bombings around the world.
After Callen catches a man breaking into his house, a former KGB operative leads the NCIS team to a shipment of counterfeit computer chips entering the United States.
Suspicious of an undercover venture involving a deal between corrupt cops and military personnel, Callen and Sam try to expose the illegal operation by posing as California highway patrol officers.
Deeks' morning routine is disrupted when he is shot during a convenience store robbery, leaving the NCIS team to investigate whether he was the assailants' intended target.
Sam resumes a former alias and boards a one-way flight to Yemen in hopes of tracking down a terrorist group's leader and rescuing the hostage son of a Saudi Prince.
NCIS investigates whether the life of a Venezuelan politician is in danger after a Navy Intelligence Commander who is responsible for tracking his moves suddenly disappears.
Kensi goes undercover as a thief in the hopes of uncovering the object that a world-class thief intended to steal.
After a rocket engine expert is killed, NCIS tech operator Eric Beale goes undercover for the first time to ensure that the classified technology used to build satellites is safe.
Deeks resumes an old alias he is not fond of in order to protect his best friend and chief informant from a criminal group that wants him dead.
After a Navy SEAL imposter is set ablaze, NCIS obtains new information regarding the whereabouts of the stolen Brachytherapy canister from a previous case that could be used to make a deadly bomb.
Hetty's sudden resignation prompts Callen and the NCIS team to investigate the reason why she would disappear in the hopes of tracking her down.
As the team travels to Romania to search for Hetty, Callen discovers new information about his past.
The NCIS team joins forces with the NSA to find the creator and controller of a software program linked to a cyber attack against the Department of Defense. Meanwhile, Callen continues searching for more information about his past.
Special Agent Sam Hanna is sent undercover as a bomb specialist as the team races to locate stolen explosives somewhere in the city. Meanwhile, to much protest, Hunter changes the dynamics of the team and has Callen partnered with Kensi and Sam with Deeks.
The murder of a news reporter leads the agents to a Libyan resistance movement; and Hetty reveals to Callen some details about his past.
The LAPD calls upon the NCIS team when a raid links a Mexican drug cartel to a wanted terrorist. Meanwhile, Sam's most prized possession is stolen.
A former Navy intelligence officer is murdered, and the agents discover his double life and a possible threat to national security.
The NCIS team must determine whether a dishonorably discharged Marine is the target of an international set-up or if he committed murder.
When a Navy ID is found on a dead body tied to a hazardous material smuggling case, NCIS is granted permission to investigate in Mexico and asked to help locate the missing materials.
After Sam’s undercover mission in Sudan turns deadly, Callen and the NCIS team must track down their missing agent before it is too late.
A botched assignment forces Hetty to fire Deeks and send him back to the LAPD. Meanwhile, an awkward goodbye between Kensi and Deeks leaves her with unexpected emotions for her old partner.
The NCIS team must locate a classified device with the power to destroy Los Angeles that was stolen from a college research facility. Meanwhile, Sam tries to track down a highly sought-after Christmas present for his daughter, and Eric meets Nell's parents.
When a researcher with the Department of Defense is found dead, Nell must put her high IQ to the test when she goes undercover as his replacement. Meanwhile, Hetty's ability to lead the team is questioned by the new NCIS Assistant Director, Owen Granger.
When a vehicle transporting Jada Khaled is ambushed, NCIS must track down the culprit to save her and their case. Meanwhile, Sam is forced to confront Jada for the first time since returning from Sudan.
After a diplomatic service van transporting an unknown package from the State Department is hijacked, the NCIS team must determine who committed the crime and what has gone missing. Meanwhile, Callen and Sam celebrate five years as partners, but face one of their biggest challenges when they go undercover for a case.
The NCIS team hunts an international killer who is able to transform himself like a chameleon to avoid capture, from country to country.
The NCIS: LA team searches for new evidence to prove Kensi Blye's innocence after she is taken into custody as the lead suspect in a murder investigation involving her deceased father's sniper unit.
Conclusion. The team try to clear Kensi Blye of murder charges, but their task is made more difficult when a private meeting between Blye and a CIA agent turns deadly.
The NCIS: LA team investigates a shooting outside the Vietnamese Consulate just prior to an international conference at the venue that the Secretary of the Navy is scheduled to attend.
When the body of a Navy Intel Officer is found, evidence points to a team of Navy SEALs who are about to depart on a hostage rescue mission, leaving former Navy SEAL Sam Hanna to interrogate the group and possibly compromise the mission.
When a former Marine is suspected of creating a chemical bomb, the NCIS: LA team joins the FBI's domestic terrorist task force including Operational Psychologist Nate Getz.
Callen and Hanna continue their pursuit of a suspect threatening to spread a deadly virus with help from Danny Williams and Chin Ho Kelly.
NCIS believes they have found a Russian sleeper cell in the middle of the suburbs, so they get Kensi and Deeks to go undercover as a married couple.
Callen and the NCIS: LA team confront their vengeful adversary, the Chameleon, when an undercover case ignites a deadly mind game orchestrated by the criminal mastermind.
The third season concludes with the team being drawn into a deadly mind game with a master criminal motivated by revenge.