At the close of the second season, Hetty had mysteriously disappeared, and the team had uncovered her whereabouts. Season 3 begins with a rescue attempt that ultimately reveals information about Callen and his family.
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 NCIS team delves into the underground world of the Libyan resistance movement following the murder of a news reporter, and Hetty reveals details about Callen's 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.
To solve the brutal murder of a Navy officer-turned-peace worker, Hetty pays a visit to an unpredictable former colleague who the peace worker was working for. He appears to try and help our team to find the killer but we soon discover he lied to our victim, making her believe she was working to help rebuild parts of war torn Afghanistan but Hetty's former colleague hid his true money-making intentions behind a smoke-screen of philanthropy. Hetty confronts her old friend who now threatens to kill her when he feels cornered. Our team jumps into action to take him down, save Hetty and expose him for what he really is.
Sam returns to the Sudan to help CIA Agent David Saleh complete their mission and gather evidence of Al-Qaeda terrorist training within the Sudan, when the body of a man turns up, the team is concerned it is Sam and Callen is sent to the Sudan. He discovers Sam is alive and the body is Agent Saleh’s. Kensi and Deeks try to find the source of the leak within the CIA before Sam’s identity is compromised. Sam stays undercover with the help of Callen and a man from the International Crime Court who is looking for evidence that the ex-Governor is responsible for atrocities against the people. Sam uses a romantic connection to Jada, the ex-Governor’s sister, to gain information. In the end, Sam's identity is compromised, but Sam gets Jada out of the country. She believes she and Sam will be together in the United States, only to be heartbroken when Sam tells her that they can never see one another again and she is forced to testify against her brother for war crimes.
NCIS:LA works alongside an LAPD task force to retrieve Semtex explosives stolen from a Marine warehouse when Deeks, trying to protect a female civilian from an Aryan thug, shots and kills him. Deeks thought the thug was going for a gun but it turns out the he was unarmed and LAPD soon breaks ties with NCIS, requiring Deeks to leave our team. Kensi is taking it the hardest, determined to clear her partner of any wrong doing. Meanwhile, Callen and the team believe there is evidence to suggest a mole in the LAPD. They think the mole assists a known gangster, Fisk, in evading any chance of LAPD building a case against him. Fisk is planning on selling the Semtex explosives to the Aryans and our team works to find the mole while Deeks feels the heat of Internal Affairs investigator, Quinn. Deeks old boss, Bates, is suspected of being the mole until Nell finds evidence that Quinn is on Fisk's payroll. Callen and the team, with Deeks seemingly working independently, rush to takedown Quinn and stop Fisk's transfer of explosives to the Aryans. Kensi finally finds out the truth that Hetty and the rest of the team knew Deeks killing of the Aryan was staged in order for him to infiltrate the LAPD. They needed Kensi to truly believe he was off the team since Bates, who was their suspected mole, was an expert interrogator and they knew he would question Kensi to see if Deeks was really off the team.
A EMP device that could disable every piece of electronic equipment in California for months, is stolen from a university, and NCIS:LA must find the thieves before they use the device and cause the death of millions. The team discovers that the professor who invented the missing "Flux" stole the device and intended to use it against the university after his funding was revoked and he didn't make tenure. He wanted to prove his theory that an EMP terrorist attack could cripple the country. Unfortunately for him, the "flux" was stolen from his car before his plan went into play and he works to help NCIS track it down before it causes mass devastation throughout California. We meet several of the professors quirky but brilliant students who all had access to the device. Callen and the team discover several of the students, drowning in student loan debt with little hope for a good paying job in this economy, hatched a plan to use the device to disable the electronic systems of a bank in downtown L.A so they can steal the money they need to pay off their loans and live a comfortable life. Callen and the team setup an elaborate sting to simulate that the device has been activated; when it really has not. They work to catch the students and buy time to deactivate the real device before it causes mass destruction.
Callen, Sam and the team are awoken in the middle of the night by Hetty's distress signal and jump into action. They know Hetty is not at any of her homes and is not responding to their messages. They locate her in the boatshed and see that she is sitting in a chair in the middle of the room but there is a shadowy figure with her. They try to devise a plan but Callen heads straight through the front door. They find Hetty sitting there perfectly fine and the new Assistant Director, Allan Granger, was the one who sent the distress call, only to test the team. Granger already is ruffling feathers but the team gets down to business when a man, Glenn Bolton, who is part of a think tank that works closely with the DOD, is shot to death. His wife is a suspect but she claims people had been following them for weeks. Granger decides to send Nell into the think tank to gather evidence on the inside. Callen and the team go to stake out the area around the think tank and speak to Bolton's wife Michelle. They discover spies posing as food vendors outside the think tank and that Michelle has been unknowingly helping one of those spies. Michelle agrees to assist them in planting a fake flashdrive that the spies think is real. The team tracks the flashdrive and manages to takedown a spy ring that was threatening national security and capture Bolton's killer. Hetty and Granger have an obvious history together and there is no love loss between them. Callen is suspicious of Granger and concerned about what his presence means for the team; Hetty assures Callen that Granger is the one who should be concerned.
Jada is being transported to finally testify in front of the Criminal Tribunal when there is an attempt to assasinate her as an SUV barrels into her transport vehicle. Our team is called in and Hetty worries that Sam may not be emotionally ready to see Jada again. Callen and the team discover that Elmslie and his family have also gone missing and fear that Khaled is behind both of these attacks. Jada gives the team the name of a contact Khaled has in L.A and they use his computer to contact Khaled. Khaled claims he is not involved but gives Sam an ominious warning that he will pay for what he has done. Eric finds the SUV that attacked Jada's transport and the team is stunned when they see surveillence footage that shows Elmslie was the driver. They track Elmslie and find that French agents, who had ties to Khaled, have kidnapped his family in order to get Elmslie to kill Jada before she reveals the French governments hand in arming Khaled. Callen and the team devise a plan to get Elmslie's family back and save Jada's life.
As Sam and Callen celebrate their fifth anniversary as partners, the NCIS: LA team investigate the hijacking of a diplomatic courier. They quickly learn the package had no value and the DSS supervisor had to be involved. They also figure out that one of the two couriers, Dunross and Clark, had to be working with their supervisor, so Callen and Sam split up the team and start probing them. Eric and Nell trace the hijacking van to a wine distributor’s and Kensi and Deeks find the contraband – it’s a $100 million worth of ephedrine, the main ingredient in crystal meth. Callen figures out that their efforts are being controlled by Assistant Director Granger, who opened up this case months ago based on an earlier hijacking. Callen and Sam decide to pose as Dunross and Clark to deliver the shipment to the Cartel. The Cartel leader orders Sam (impersonating Clark) to kill Callen (Dunross), thereby confirming Granger’s theory that Clark was the guilty courier. However, Callen and the team find evidence that proves Dunross was the mastermind of the whole scheme, thereby one-upping Granger.
NCIS: LA is called after two pharmaceutical executives are brutally murdered by Zahid DeGramont, a man believed to be the head of a French-Moroccan arms gang who is wanted in two other countries. Assistant Director Owen Granger introduces Sam and Callen to Interpol Agent Martin Källström, who has been tracking DeGramont across the globe. Confused, Callen informs Källström that DeGramont was killed in a raid that he led six months ago, but Agent Källström insists they investigate further given the similarities in the murder methods of the various cases. Sam and Callen go to visit Karim Ghilas, DeGramont's driver who Callen shot in the face in the raid; but the man they find is an imposter. After piecing bits of the puzzle together, the team figures out that the real murder's M.O. is that he's a Chameleon; someone who meticulously changes his identity for every crime he commits. They follow the clues to a nightclub and try to stage a bust, but the Chameleon turns the tables on them and sends them a video of Agent Källström being shot and burned alive in his car. When Eric contacts Interpol to inform them that one of their agents has been killed, the team learns that the Agent Källström they had been working with was an imposter, as well. Sam and Callen then follow a lead to a hotel, where they arrive just in time to see the fake Agent Källström die from poisoning. Callen then gets a call from the Chameleon, who tells him that he knows everything about Callen and will kill him one day as revenge for shooting him in the face. In the end, the real Chameleon escapes, leaving Callen anxious for his safety.
The NCIS:LA team is shaken when Assistant Director Owen Granger interrogates Kensi after the suspicious death of Marine Sergeant Chris Blake. Blake used to be the spotter for Kensi's father, Donald Blye, a special ops sniper, and it appears that his death was no accident. Blake is the latest in a string of mysterious deaths of men who were part of Donald Blye's unit, and it is revealed that Kensi was the last person to talk to many of them, making her the prime suspect in the case. Kensi is taken into custody while the team searches for a way to prove her innocence, but she escapes and sets out on her own to find the real killer. Sam and Callen follow the evidence and track down Alec Harris, a CIA agent and former handler of Donald Blye's unit who claims to have information about Donald's death. The catch: he'll only speak with Kensi. The team sets up a meeting with Kensi and Alec at the old Griffith Park Zoo, but it's interrupted by an unseen sniper who kills Alec and manages to hit Kensi in the chest.
After narrowly avoiding death while investigating her father’s murder, Kensi sets off on her own to track down the man responsible, only to run into her estranged mother who she hasn’t seen in 15 years. When the team figures out that one of the member's of Kensi's father's unit faked his own death, Granger backs down from his suspicions of Kensi. Callen and the rest of the NCIS:LA team races to find their killer and stop Kensi from doing something she'll regret or worse, is killed.
When a young Vietnamese man is shot approaching the Vietnamese embassy, Callen and the team are charged with protecting the embassy. There's an upcoming Pan-Asian conference being held there and they've received several terrorist threats. While investigating the shooting, Kensi and Deeks uncover a human trafficking ring being run by Yen Tan, a woman who owns a shirt manufacturing company. Initially believing she was behind the threats, our team discovers her husband, Binh, reviled her ruthless ways and saw all capitalists as evil. Binh is the militant behind the threats and they’re able to stop him before he bombs the embassy. During the course of the investigation, NCIS:LA uses a Vietnam Vet as an interpreter who discovers his daughter and grandson were some of the couples victims and they manage to reunite the family.
When a SEAL is found murdered on a training base, the NCIS team is sent to investigate. The murder weapon appears to be a specialized knife used largely by SEALS and when Callen suggests the killer may be a fellow SEAL, Sam defends them. Against Sam's protests, Callen asks that the victim's SEAL team be held back from their next mission: rescuing two Americans being held hostage on the border of Afghanistan-Pakistan border. It’s a time sensitive mission and this team has previous experience in the region, making them the only choice to execute the rescue mission. Tempers run high as Callen tries to question members of the SEAL team. They also uncover evidence that the victim may have been selling secrets to the enemy. Sam gets one of the members to confess to injuring the SEAL in self-defense when they confronted him about being a traitor, but the death was ultimately the result of the victim’s asthma. As they reach the go/no go point in the mission, Callen and Sam decide to release the team stating they found no evidence of a murder. They manage to rescue the hostages but with some casualties due to the fact their mission had been compromised by the traitor.
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. Peter Cambor guest stars.
The joint NCIS: Los Angeles and Hawaii Five-0 task force travel from Hawaii to Los Angeles, when the lead suspect in the case moves to the mainland with a deadly virus in tow.
Kensi and Deeks are sent undercover as married couple Melissa and Justin when evidence points to a Russian sleeper cell in a suburban neighborhood.
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 L.A. team is drawn into a deadly mind game against a master criminal motivated by Revenge.