When a Russian bomber goes missing while flying over U.S. soil, Callen and Sam must track it down in the desert and secure its weapons and intel before the Russians on board destroy the plane. Also, Nell returns to OSP following her mother's death after Hetty asks her to fill in while she is away. While there, Nell learns that FBI Agent Roundtree has officially joined the OSP team, and that Eric's technology work has resulted in him being away from OSP.
As the trial begins of Chief Petty Officer Thomas Argento, the SEAL whom Callen, Sam, and Roundtree arrested for war crimes last season, the NCIS team is called to help find the missing star witness.
When Nell sends Sam to meet an informant who plans to blow the whistle on a military secret, Hanna's life is in danger when the man tries to run him down and kill him. Also, Kensi and Deeks debate whether or not to buy their first house.
The body of a murdered Navy reservist is found by thieves in the midst of a robbery and NCIS must work with the burglars to find the killer. Also, Kensi and Deeks struggle to decide if they are ready to make the leap and buy a house.
In order to get critical intel on a matter of National Security, Kensi must come face to face with David Kessler (Frank Military), a sociopath who has been obsessed with her since she put him in jail years ago. Deeks is desperate to keep Kensi safe, but he must leave NCIS after his liaison position is abolished by LAPD amidst major department realignments. Ultimately, Kessler is released from prison via a Presidential Executive Order, leaving Kensi a major target.
Before Christmas, Hetty assigns Callen the case of his former foster brother and his wife who, upon reentry into the U.S., are framed for smuggling drugs across the border in her oxygen tanks. Eric returns to OSP to assist with the case, though his increased eccentricity leaves his former coworkers amused. Meanwhile, as Deeks attempts to become an NCIS Agent in the wake of his liaison position being terminated, he is informed by Hetty of his acceptance to FLETC.
The NCIS team's murder investigation of a man who sold military information leads to the abduction of a doctor whose cutting edge neurotechnology could be developed into advanced weaponry. Team members are interviewed by FLETC to see if Deeks would make a good NCIS agent. Callen tries to have an important talk with Arkady regarding his future with Anna.
When NCIS investigates the murder of a man about to reveal the source of a massive counterfeiting operation, an old acquaintance becomes their prime suspect and reveals the true reason for her return. Deeks struggles at FLETC during training to become an official NCIS agent.
While NCIS must track down an organized crime leader who is trying to buy stolen defense technology, Callen goes to Anna to ask the ultimate question, only to be met with a shocking revelation. Deeks is kicked out of NCIS training only to find Hetty has a life-changing surprise for him - he has been made an NCIS investigator.
When Sam's daughter Kam is abducted after leading citywide protests, the NCIS team rushes to prevent another family tragedy in Hanna's life from occurring.
When Callen goes to the National Counterterroism Center on the pretext of interrogating a Russian asset from the crashed plane case he investigated months earlier, the tables are turned and he is detained, accused of being a Russian agent.
After Callen receives a cryptic message from Hetty, he tracks down the person trailing him, bringing him to a remote location teeming with Russians…and face to face with Anna.
To rescue Joelle from further torture by the Russians, Callen and NCIS must offer up Anna as bait to Katya. Callen finally discovers who accused him of being a Russian spy.
After Anna is kidnapped, Callen and the team must race to save her before she is shipped back to Russia. Nell is offered an opportunity by Admiral Kilbride. Kirkin is killed in a gun shoot.
NCIS obtains a hard drive containing a realistic deep fake video of a deceased terrorist and must retrieve the dangerous technology behind it. However, when the team's communications are hijacked during their mission, they find that several of their own has become a victim of its potential.
When military-grade technology is stolen, a deaf engineer who always wanted to serve her country, and the only member of her team to survive the theft, helps Kensi and NCIS track down the tech before it's taken out of the country.
When a Naval Intelligence Officer is tortured and murdered, NCIS must work with Joelle who informs them that other CIA operatives are being killed in the same way while Kensi receives a threatening postcard from David Kessler, the sociopath who is obsessed with her.
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. Nell faces a crossroads when she is given two choices: officially return to NCIS or accept an offer from Eric to work with him at his tech company. Ultimately, she decides to work with Eric, saying an emotional goodbye to Hetty, who has returned to Los Angeles under mysterious circumstances.