The NCIS: LA team find out that one of their own has been compromised as they investigate the murder of a Navy contractor involved in illegal transactions of confidential data.

After Callen’s father, Garrison is found in an NCIS patient’s hospital room during a radiation poisoning case, Callen must take him to the boatshed for interrogation. Also, the team discusses their Thanksgiving plans.

Following the kidnapping of Sam's wife, Michelle Hanna, Sam goes rogue from the NCIS team and attempts to stop his arch nemesis Tahir Khaled from ever targeting his family again.

Season 9 begins with Hetty turning in retirement papers and disappearing. A new executive director arrives and immediately makes staffing changes. Meanwhile, Sam, still mourning his wife’s death, insists that Callen find a new partner.

The team must find assailants who illegally crossed the border and attacked California Highway Patrol officers; Homeland Security sends Nell's older and bossy sister to assist with the case.

Callen, Sam, Kensi and Deeks join Hetty’s team from the Vietnam War, Sterling Bridges, A.J. Chegwidden and Charles Langston, in a dangerous and off-the-books rescue mission to save Hetty from her captors in Vietnam. Also, Mosley calls in Nell’s sister, homeland security specialist Sydney Jones, to assist the team in Los Angeles with processing evidence connected to Hetty’s time in Vietnam.

Callen and Sam travel to the USS Allegiance in the Persian Gulf to work with Navy Captain Harmon "Harm" Rabb, Jr. (David James Elliott) when the NCIS team uncovers ISIS sympathizers who are targeting military locations.

After a rise in deaths caused by black market opioid use, the NCIS team links the street drug to funding for terrorist activities

Deeks is kidnapped by an associate of Kirkin’s in need of his help and NCIS investigates the shooting of a militarized dolphin equipped with a Russian microchip. Also, Beale makes Nell an interesting offer and Hetty returns.

The NCIS team helps a U.S. ambassador search for her missing daughter, Gia, a popular social media influencer. Also, Agent Aliyah De León returns to support the team with the case.

The NCIS team helps Naval intelligence officer Akhil Ali locate a fellow officer who went missing while recruiting foreign assets as potential sources of intelligence. Also, Callen and psychologist Nate Getz track down a man Callen believes was present for his training when he was young.

The NCIS team hunts for a heist crew that robs a Los Angeles casino with military-grade power. Also, Kensi and Deeks hear exciting news regarding the adoption and Callen takes a big step in his relationship with Anna.

When an ATF agent goes missing, the agency seeks help from the NCIS team to investigate stolen military-grade weapons and locate the agent. Also, Callen and Anna continue to plan their wedding, Rountree’s sister interviews for medical school, and Sam encourages his father to take part in the drug trial.

The NCIS team continues the case with ATF and the stolen weapons. Also, Callen and Anna decide on an impromptu wedding.