While the team investigates the theft of a computer virus, Callen and Sam consider their future at the agency, Kensi and Deeks discuss having children, and Eric and Nell analyze the impact of Eric's undercover assignment on their relationship. Also, the team tracks Mara, a crooked upscale banker
After a Navy lieutenant disappears from the scene of a car accident, the NCIS team processes the crime scene and discovers his laptop is missing along with recently accessed confidential information for retired Navy SEALs.
The NCIS team links the theft of an undersea drone prototype to a video game streamer's elaborate party; Callen and Sam cross paths again with insurance broker Katherine Casillas, who insures the gamer's property.
The NCIS team reluctantly aligns with two former criminals from England, Ricky Dorsey and Frankie Bolton, after a powerful arms dealer kidnaps Ricky's daughter in an attempt to obtain a dangerous weapons system.
While Callen and Sam are aboard the USS Allegiance, the ship is placed under quarantine for possible Ebola exposure. Also, Kensi and Deeks investigate the murder of a petty officer who recently departed the USS Allegiance and is linked to the Ebola exposure.
In the Season 11 premiere, Callen and Sam work with Navy Capt. Harmon Rabb Jr. to apprehend spies aboard the USS Allegiance. Also, Hetty partners with Marine Lt. Col. Sarah "Mac" Mackenzie to neutralize a missile attack in the Middle East, and Kensi and Deeks are trapped in a mobile CIA unit in Iraq while under attack by ISIS.