While investigating the theft of cesium from various hospitals, the team gets impaired by the arrival of Undersecretary of Defense Corbin Duggan, who intends to reorganize the department in the wake of their inability to find the mole.

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The team travels to Syria to capture a high-value target, but the mission goes awry when their chopper is shot down, leaving Kensi badly injured and the rest of the OSP team must work around Duggan to ensure they get out alive.

The team investigates an abduction case while down two members, with Hetty being held in D.C. for questioning, and Kensi still in the ICU following the mission in Syria

After a Homeland Security agent is poisoned, the team's investigation leads them on the path of a Triad assassin and a possible traitor.

The murder of a navy machinist with high security clearance sends the team on a city-wide hunt tracking evidence. Also, Anna Kolcheck (Bar Paly) partners with Callen, and Sam assists Hetty in the ongoing mole investigation.

While investigating a failed break-in, the team discovers that the man responsible for stopping the break-in is more than he seems - and that he is a former Mossad agent targeted by a rogue comrade. While Anna partners with Nell on the case, Deeks tries to help Kensi deal with the extensive therapy required for her recovery.

After an NSA analyst is found eaten by a shark, the team's investigation leads them to a cartel's money-laundering scheme and sends Callen into a mental asylum to find a key witness; Kensi struggles with her therapy.

The team's investigation into the electrocution of a college student working on a classified Navy project leads them to his inquisitive daughter, who may be the key to accessing his work.

After a woman is poisoned with polonium-210, the team's investigation into her past leads them to Callen's father - and his dark secrets.

After two fake sheriff's deputies are killed outside of Callen's house, the investigation leads them deeper into the mole problem, and Nell interrogates Carl Brown for more information.

The team goes on the chase for a Navy analyst being held hostage, only to discover things aren't as simple as they seem.

After a city councilman's bodyguard is killed, Sam goes undercover inside the bodyguard's employer to figure out what got him killed.

On the day Undersecretary Duggan comes for Hetty's resignation, the team finds itself short-handed as Granger, Deeks, Sam, and Callen are arrested for planted evidence. While in custody, Granger is stabbed by an unknown assailant.

While Hetty goes rogue on her own agenda to identify the mole, the team must regroup, but things go awry when Kensi is kidnapped by a man she thought she could trust.

As the team races to save Kensi from Ferris/Sullivan, they find themselves questioning who they can trust when old faces resurface.

Note: This is the final appearance of Owen Granger due to Miguel Ferrer's death.

When a Navy lieutenant and his grandfather are kidnapped from a retirement home, the team's investigation leads them to a con artist couple and the hunt for a rare coin; Callen meanwhile has to deal with his father's actions when he kidnaps the father of his grandson (and Callen's nephew).

Note: Owen Granger is written out of the show in this episode due to the death of Miguel Ferrer. Granger is said to have left the hospital and the team to "tend to some old business" and an in memoriam slide for Ferrer is displayed before the closing credits.

Sam resumes an old alias to bring down a major criminal kingpin; Callen and Anna's romantic night is interrupted when they are tasked with escorting a high-value prisoner to Los Angeles for questioning.

After the U.S. Treasury Department is hacked, Nell and Eric go undercover inside a couple's retreat to track a tech-savvy husband and wife linked to the crime. Also, Digital Forensics Specialist Dave Flynn (Scott Grimes) arrives from the NCIS cyber office in San Diego to run ops while Eric and Nell are on assignment.

After a design engineer for a new Navy stealth vessel is killed, Callen and Sam board a flight to Tokyo to follow his colleague, who may have the stolen plans on him.

The team investigates when a man claims his wife, a Navy contractor is selling state secrets, leading them to a Cuban club where Kensi and Deeks go undercover.

When a veteran kidnaps a corrupt VA administrator, the team must work with old friends of Hetty's, one of which being A.J. Chegwidden to find him and figure out what's going on.

The team works with Hetty's former Vietnam War colleagues to recover $40 million in stolen gold, though things get complicated when other parties invest themselves into the search. Deeks receives some surprising news from Detective Whiting about his IA case.

The team races to rescue Michelle when she is kidnapped, with the kidnappers demanding the release of Sam's nemesis Tahir Khaled.

After Michelle's death, Sam goes off on his own to avenge her death and end Tahir Khaled once and for all.