The Special Projects team travels to Romania to search for Hetty, while delving into the history of the Comescu crime family, and their connection to Callen. Hetty confronts Alexa, matriarch of the Comescu family, and it is revealed that Callen's grandfather was an OSS agent who killed several members of the family; the Comescus retaliated, killing his mother, but leaving Callen and his sister alive. Meanwhile, Eric and Nell discover that Lauren Hunter, the Office of Special Projects Operations Manager, is a member of the Comescus. It is ultimately revealed that Hunter assumed the identity of Ilena Vadim - a member of the family who distanced herself from them - to infiltrate the Comescu family; the other members of the team are unaware of her exact allegiance until she kills Alexa and retrieves a laptop from the Comescu beach house. The episode ends in a cliffhanger with the other characters realizing that Hetty has been shot by Alexa. She then collapses to the ground, her fate unknown.

The NCIS team has to join 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. The episode ends with Callen confronting Hetty about her knowledge of his past and family.

Operations Manager Hunter rotates the investigative partnerships during an investigation into the death of a Marine who died during an explosion.

As Hetty returns to work the team investigates a death tied to the Libyan resistance movement.

The LAPD calls upon the NCIS team when a raid links a Mexican drug cartel to a wanted terrorist affiliated with al-Qaeda where it is discovered that the terrorist plans to sell a captured MQ-9 Reaper to the cartel. Meanwhile, Sam's most prized possession is stolen.

After a former Navy intelligence officer is murdered, Hetty contacts a former co-worker when the NCIS team uncovers a threat to a pipeline in Afghanistan. The victim was killed to prevent disclosure of the attack.

When a Marine that was dishonorably discharged is accused of murder and claims he was framed, it is up to NCIS to figure out the truth.

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. The episode ends with Sam heading off to Sudan to work alongside a CIA task force.

After Sam's undercover mission in Sudan turns deadly with a body presumably matching that of Sam's description, Callen heads off to Sudan to discover the truth and to track down Sam before it's too late. Meanwhile, back in Los Angeles, the NCIS team searches for clues in regards to the case but things go wrong when Sam's cover is blown, forcing Callen and Sam into a fight for their lives.

When Deeks shoots an unarmed man during a joint NCIS/LAPD operation, LAPD blames NCIS for ruining the operation and breaks ties with NCIS, forcing Hetty to eliminate Deeks's liaison position. However, the shooting was a ruse enabling Deeks to return to LAPD so that a mole in LAPD could be identified. With the mole eventually identified, Deeks returns to his work with NCIS.

During the middle of the holidays and the distractions they cause, the team is tasked with finding the thieves who stole an experimental electronic device with enough power to destroy half of Los Angeles.

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.

The team must find the person behind an ambush on a vehicle carrying Jada Khaled to save her and their case; Sam must face Jada for the first time since Sudan. The humanitarian agent from their previous mission was revealed to have been forced to ambush Jada Khaled after members of a French company who possessed ties with the Sudanese dictator kidnapped his family and threatened to kill them if he didn't kill her.

The team investigates a hijacking when a package from a state department van goes missing. Meanwhile, Callen and Sam celebrate five years as partners.

The team investigates the murder of two businessmen and later finds out that a spy/agent named Chameleon who can take on any personality or facade he likes is responsible for the killings. When the Interpol Agent the team was working with is murdered, Granger takes over the case, forcing the team to report to him while still resenting his involvement. But despite their best efforts, Chameleon manages to evade them but not before calling Callen from an unknown location and then telling the NCIS Special Agent that he's going to kill him. Later, under pressure from both Hetty and Callen, Granger finally tells them the reason for him coming to Los Angeles: he's here to catch a killer and the camera then shows him looking over at Kensi, suggesting it might have something to do with her.

Kensi is taken into custody by Assistant Director Granger when various Marines from her deceased father's unit end up dead in various car accidents. Granger reveals Donald Blye's unit was actually a Black Ops Hit Team and that everyone in the unit has been killed, with the only common link between them being Kensi. However as Callen and the team investigate to try and clear their friend's name, they uncover Granger's ties to the unit and begin to suspect that he is the true killer. The episode ends in a cliffhanger with Kensi being shot by an unknown sniper and it is not yet known if she is alive, having been injured by the bullet, or dead.

Kensi is injured, but survives the shot from the sniper and goes rogue. Callen & co discover that Granger fled the scene, and they must find him and get answers whilst Kensi continues the chase for the killer responsible for her father's death as she resolves to solve the case once and for all.

The team investigates a shooting outside the Vietnamese Consulate just before an international conference at the venue that the Secretary of the Navy is scheduled to attend. But they soon find evidence suggesting that an illegal sweatshop might be a cover for a human trafficking ring or terrorists.

A Navy Intel Officer is found dead, and all evidence points to a team of Navy SEALs who are about to depart for a hostage rescue mission. Sam is chosen to interrogate the group which may compromise the mission.

When a former Marine is suspected of creating a chemical bomb found in a vehicle, Nate Getz returns to Los Angeles and the team must work together with the FBI to track down and stop a domestic terrorist.

Detectives Danny Williams (Scott Caan) and Chin Ho Kelly (Daniel Dae Kim) of the Hawaii Five-0 task force arrive in Los Angeles to help Callen, Sam and the Office of Special Projects find and stop Jarrod Prodeman (Rob Benedict), a disgraced doctor carrying several vials of smallpox, capable of wiping out half the world's population. They eventually find and capture Prodeman, who reveals he has already sold the vials to a Doctor Rachel Holden, who is nowhere to be found. Research soon finds that Holden, who believes that the Earth's population has grown too huge in the last thousand years, is planning on unleashing the smallpox to cut the population in half so that the Earth itself could recover.

Guest starring: Rob Benedict, Laura Regan, Cynthia Addai-Robinson, Helen Eigenberg, Celia Finkelstein

Deeks and Kensi go undercover as a married couple to catch a Russian sleeper agent in the neighborhood. Through many suspects and an unexpected twist for Deeks and Kensi, they eventually capture the agent. Also, Kensi and Deeks share a kiss to protect their cover.

The Chameleon lures Callen and the rest of the team into a deadly mind-game with things becoming even more personal for the team when both Agents Mike Renko and Lauren Hunter are killed.

The Chameleon's mind games continue and things heat up when the team discovers an innocent man's life is at stake. The episode ends with Callen being arrested by the LAPD after killing the Chameleon in revenge for Renko and Hunter's deaths. At the same time, Hetty is seen leaving a resignation letter for Owen Granger on her desk, suggesting that she fully intends to leave OSP for good due to the incident.