While a sniper wreaks havoc across New Orleans, the team must also deal with Brody's unexpected departure and FBI Special Agent Gregorio's arrival to investigate the team.
The team investigates a homicide case that puts the blame of Pride's Navy Intelligence friend Elvis in the middle. Meanwhile, the FBI continues to internally investigate Pride's team following Brody's departure and Russo's death. The FBI takes over the case, despite a victim being a Navy officer, but Pride's team refuse to budge and find key evidence, forcing the FBI to collaborate. Gregorio is ordered to work with NCIS to bring down the cartel.
The team is put in a difficult position to help rescue a Navy petty officer being held captive in Mexico. Meanwhile, Gregorio's put in a tough spot when she begins to work with Pride's team and reports back to headquarters about his team's actions.
As his mother visits, Sebastian is kidnapped and forced to hack into a federal detention center to help break out a serial killer and escape with him to the border.
Pride and his team investigate a plane crash that killed three plane crew and three petty officers who were passengers, which later turns out to be murder and involves the CIA. Meanwhile, LaSalle and Percy interview candidates to replace Brody. Gregorio considers whether she should stay in New Orleans or return to D.C.
When a SEAL-in-training is found dead after he's reported UA, the team discovers a dark secret he was hiding about his past—and a conspiracy that goes up to Mayor Hamilton. Meanwhile, LaSalle tries to evade an old flame, who has a big surprise for him. Elsewhere, Dr. Wade tries to get Pride to convince Danny to go to college rather than join the Navy.
The team investigates the murder of a biker who was a sailor from Mississippi and later find that it might be the start of an old rivalry between two biker gangs. Percy goes undercover to find her old informant who's working for one of the gangs. Gregorio encourages LaSalle to talk to Pride about his newfound fatherhood.
A petty officer and member of the prestigious Navy band is found murdered, and her nephew is the only witness to the crime. Pride must try and get the boy to trust him and open up while trying to find out why she was killed. Meanwhile, Percy finds out about LaSalle's child and says he needs to get his life better organized. Elsewhere, Gregorio is conflicted between returning to Washington, D.C., and leaving the FBI to stay in New Orleans.
The team investigates a Marine and race car enthusiast who was killed in an accident, but Pride suspects foul play. Meanwhile, LaSalle receives news that Tucker isn't his son and his real father is coming for him. Despite the lie, LaSalle decides to help Melody get safely away from him. Also, Gregorio is helping Assistant U.S. Attorney Hannah Lee build a case against Garcia.
Pride and his team investigate a family friend's fiancée who is also a leader in a major drug smuggling cartel. Gregorio's conflict of interest continues as she disobeys orders from her FBI director to help NCIS bring down the cartel.
Pride takes matters into his own hands without the FBI’s involvement to catch Garcia. The team volunteers to help knowing the consequences of their involvement. Pride suggests that Sebastian go undercover to take down Garcia.
Pride's team works around the clock to save him from a major explosion on an oil rig, as he tries to capture suspected murderers who work on the rig. Gregorio begins her first day as an NCIS agent. Meanwhile, Sebastian starts his training to be a field agent.
After thousands of classified government files are stolen, the NCIS team searches for an underground group of hackers co-founded by Pride’s old contact, Elvis Bertrand, who are known for exposing corruption among prominent people in New Orleans. Also, Sebastian joins the team as a newly minted NCIS Special Agent.
At the behest of Special Agent Leroy Jethro Gibbs, Agents Timothy McGee and Nicholas Torres travel to New Orleans to assist Pride and his team in the retrieval of a stolen terror playbook, an operation assisted by Torres and Gregorio from the field position.
The team investigates the grisly murder of a petty officer. Wade realizes it might be the same killer she testified against and helped send to prison 20 years ago, who was recently released and might want revenge. Later on, the killer is captured but claims to be innocent. Pride looks into the last murder and suspects that the "killer" had been framed both times.
Pride's longtime friend, state and military attorney Rita Devereaux asks NCIS to investigate the disappearance of a JAG lawyer who specializes in classified cases and volunteers at a private military academy.
Pride's team goes on a manhunt to capture a highly skilled Marine with no criminal history after he assaults six civilians in a bar. However, the case becomes more complicated when it turns out the Marine's wife has been abducted by a woman's trafficking ring.
Gregorio's ex-husband, who disappeared after embezzling more than $80 million from the Hurricane Katrina relief fund, comes to New Orleans after Pride's team found a connection with him and a murder investigation.
While investigating a deadly accident at a naval base, the team discovers a unit of Seabees was poisoned with a contagious super virus leaving the rest of the base and the entire city of New Orleans at risk for a catastrophic outbreak. During the autopsy, Wade is infected with the virus and given hours to live if an antidote can't be found.
LaSalle's old partner at the New Orleans Police Department's Vice Squad (Jeremy Ratchford) comes under investigation when drugs from NOPD evidence lock-up are discovered on the streets and smuggled onto a Navy ship. Meanwhile, Pride and Rita discuss their relationship as she delves into Hamilton's connection to the impoverished Clearwater neighborhood.
Pride's team puts their careers at risk when Pride puts a wiretap on Mayor Hamilton's cell phone to help bring him down while the team investigates the mysterious theft of Navy weapons.
After the Belle Chase Navy Chaplain and pastor at Clearwater Baptist is murdered, Pride believes he found a connection between Mayor Hamilton and the illegal activity taking place in the city of Clearwater. Also, Percy continues to face repercussions of her choices on a previous case.
After a tail on one of Hamilton's men goes horribly awry, the team faces the political backlash demanding they stop their investigation or else.
Pride is forced to fake his death and go rogue in order to capture Hamilton and confront him about his crimes. Meanwhile, the rest of the team enlist the FBI assistant director to help track down Pride.