Following an ambush on a Navy convoy, the team discovers that a sophisticated GPS-guided missile has gone missing. They track the theft to a massive meeting of anti-government militia groups, with Pride going undercover to learn what they intend to do with the missile. Meanwhile, Percy adjusts to NCIS, having become an NCIS Special Agent while being pranked by Brody and LaSalle. Elsewhere, Pride's divorce is finalized.
The team investigate a murder of a blogger who obtained a top secret government file. It is later revealed that a trained Navy SEAL might be behind the crime and also a possible war crime.
When a female combat pilot and Navy hero dies in an air-show plane crash, the NCIS team must investigate if it’s the fault of the pilot or the new jet that was just approved to deploy to bases globally.
The team investigates the murder of a Navy drone pilot. Later on, it's revealed that the pilot was using a black market drone to obtain military files which could be linked to the murder. Meanwhile, Pride confronts LaSalle about his self-destructive behavior after Savannah's murder.
Special Agent Pride is sent a partner from the Australian Defence Force Investigation Service, Special Agent Naomi Parsons, after an Royal Australian Navy Lieutenant, who was key to international negotiations on nuclear weapons, is murdered in New Orleans.
The team investigates the murder of a petty officer while they participate in a Red Dress Run for charity. It leads them to an epidemic of a new drug called Flakka, which then leads them to one politician as the culprit.
The team investigates the murder of two Navy paramedics and searches for a missing organ for a recipient. Meanwhile, Brody's mother Olivia comes to visit and joins the team to help with the case.
Pride and Percy are caught in a violent crossfire while escorting a Texas prisoner as a key witness to a murder trial. The team later discover that old enemy Zed Hastings (from "Sic Semper Tyranis") has set a trap in order to get Pride.
The power in New Orleans goes out while the team investigates the murder of a petty officer who was engaged to a friend of Laurel Pride.
The murder of a Marine provides new clues in the first case Pride and Lasalle ever worked together, just before Hurricane Katrina struck the city and washed away any evidence. Also, the team celebrates Thanksgiving together in Pride’s bar.
At Christmas, the team investigates the death of a Navy officer's wife during a home-invasion burglary. Wade's loyalties to job and family come into conflict when her adopted son Danny is implicated in the crime and arrested.
After events in "Sister City (Part I)," armed Russians search but don't find Counselor Pavlenko's body in Chief ME Dr. Donald Mallard's van; a ruse. D.C. NCIS Special Agent Eleanor Bishop travels to New Orleans with Pavlenko's body so Dr. Wade can investigate further. Washington NCIS Senior Special Agent Leroy Jethro Gibbs reads-in Pride on Blye Industries-DoD project "Manta Ray," a next-gen stealth warship. Russian GRU sleeper agent Eva Azarova, who is involved with Forensic Specialist Abigail
The team investigate a murder made to look like a suicide of a Navy petty officer. Meanwhile, the team set up an online dating profile for Pride.
In the midst of Mardi Gras, Pride and Mayor Hamilton are abducted from their parties. While the team races to locate them, the two find themselves with the husband whose wife's supposed suicide was investigated by Pride, and Hamilton was suspected of killing her.
When a mystery man saves the life of a Lieutenant and then disappears from the scene, the NCIS team unravels a new case when forensic evidence suggests he is a soldier who was captured in Afghanistan years ago and never found.
After tracking stolen Navy TNT to a cocaine warehouse, Special Agent Pride and the NCIS team uncovers a domestic drug ring that is producing their own cocaine and headed by Sonja’s childhood friend, Marion Watkins.
After a Navy captain's murder is broadcast over the radio, the team's investigation leads them to protect the radio host and look into her charity. Meanwhile, Pride's daughter makes a surprising decision about her future.
The team investigate a deadly traffic accident that provides a new lead to the murder of Brody's sister.
The NCIS team discovers a surveillance van filled with photos documenting Special Agent Pride’s every move after his daughter Laurel is attacked on campus and placed in protective custody.
The NCIS team investigates the murder of a Navy Lieutenant during a French Quarter second line funeral procession, a New Orleans tradition that celebrates the recently deceased with a musical street parade.
The jobs of Pride and his team are in jeopardy when they investigate the murder of a naval supply officer with whom an army general was supposedly having an affair.
The NCIS team investigate a suspicious explosion at a popular restaurant in New Orleans that targeted a Navy culinary specialist. Meanwhile, Brody is questioned by the FBI about the General Matthews case and meets a DHS official.
The NCIS team works with Homeland Security on a case involving the murder of a Navy master diver, which they later link to a plot of a terrorist attack in New Orleans.
While tracking down stolen explosives, Brody suspects that the Homeland Security agent assisting them is the ringleader of the plot. Note: This episode marks the final appearance of Zoe McLellan as a series regular.