The New Orleans team investigate the discovery of a severed leg found at a marina with the leg later revealed to have belonged to a recently murdered Navy Petty Officer Second Class who Pride mentored, prompting the team to investigate the crime. Brody, having joined the NCIS: New Orleans team on a permanent basis (in the NCIS season eleven episode, "Crescent City") is trying to get acquainted with New Orleans. NCIS Medical Examiner, Dr. Donald "Ducky" Mallard later offers both Wade and Pride some insight into the case.

Guest starring: James McDaniel, Matt Bushell

When a Navy lieutenant on liberty dies in downtown New Orleans after being hit by a taxi, the team investigate what happened, but things soon take a turn when the autopsy reveals that the victim died of the bubonic plague and that the death is connected to a potential bioterrorist attack on a Navy ship, the U.S.S. Geronimo. As the team begin rounding up those assigned to the ship, they receive assistance from NCIS Director Leon Vance with CDC officer Carol Wilson and NCIS Special Agent Anthony "Tony" DiNozzo both arriving in New Orleans to help with the case.

Guest starring: Meredith Eaton, Erika Alexander, James Eckhouse, Annika Marks

When a bus crashes into a ditch resulting in three prisoners who were en route to the Naval Brig in Charleston escaping and the deaths of two security guards and a prisoner, the team soon discovers that one of them is a wanted criminal who poses a threat to national security. NCIS Director Leon Vance and Pride's friend, fellow NCIS Special Agent Leroy Jethro Gibbs both assist in the search with the investigation.

Guest starring: Felisha Terrell, Joe Massingill, Evan Gamble, Charlene Amoia, Cliff Simon

After a Navy SEAL is found shot dead in a sorority house, the team must determine if the motive pertained to one of his classified missions or foul play, only to discover an illegal prostitution ring is operating in the college on behalf of the local Russian mafia branch. Meanwhile, Pride's daughter, Laurel, pays the NCIS office a visit.

Guest starring: Vanessa Marano, Dora Madison Burge, Gino Anthony Pesi, Alexander DiPersia, Hunter Burke

When a chief warrant officer who specialized in counterintelligence is found dead from waterboarding, the team discover that the victim's wife has been kidnapped and is being held for ransom. FBI agent Tobias Fornell arrives in New Orleans to assist Pride and the team with the case.

Guest starring: Gabriel Olds, David Burke, Dorian Brown Pham, Chelsey Crisp

As New Orleans prepares to celebrate Halloween, a Naval Staff Judge Advocate is found in a cemetery murdered "vampire-style" with the team discovering that an unlikely suspect is responsible and that a woman's life is hanging in the balance. Meanwhile, Brody and LaSalle compare costumes.

Guest starring: Paige Turco, Rodney Rowland, Eyal Podell, Adam Rose, Aubrey Deeker Hernandez, Cyd Strittmatter

A Navy officer with the highest-level top secret clearance is murdered after being assigned as a tech liaison with a private developer, with the team also discovering his assistant dead in the bath at his house. Meanwhile, Pride transforms the carport into an auto shop when he works on the first car he gave his wife.

Guest starring: Laura Allen, Melinda Page Hamilton, Adam J. Harrington, Andrew Borba

A petty officer is found dead in a Mardi Gras float storage facility with an engagement ring and proposal plan in hand. The investigation takes a mysterious turn when the team are unable to locate his supposed long-term girlfriend, but things change when it's revealed that a murderous Colombian assassin is in the city and plan on killing a group of Navy and Marine personnel who hope to stop the flow of drugs into South America.

Guest starring: Wes Brown, Kyle Davis, Shawn Carter Peterson, Matt Riedy

The team investigates a 40-year-old cold case about a murder of a chief petty officer which hits close to home for Dr. Wade. However, an exhumation of the body reveals some unexpected evidence that may change everything. Meanwhile, Sebastian gets into the Thanksgiving mood and Laurel brings home her boyfriend.

Guest starring: Tim de Zarn, Cristine Rose, Jeff Kober, Angela Gots, Roberto Aguire

A former SEAL who hunts military impostors is found dead at a museum, and the team's investigation leads them to find the jacket of a Marine who was presumed killed in Afghanistan. When the investigation reveals that the Marine may still be alive, both Pride and LaSalle travel to Afghanistan in an attempt to bring him home. Meanwhile, Brody wonders about LaSalle's issues with Christmas.

Guest starring: Felisha Terrell, Brea Grant, Jim Gleason, Leslie Castay, Katy Sullivan

While attending the Navy-Marine Relief Gala, a deadly explosion happens, putting Pride's daughter's boyfriend in the hospital. The team learns that Pride was the intended target and the assassination attempt could be related to one of his old cases.

Guest starring: Roberto Aguire

The NCIS team partner with the Coast Guard Investigative Service Special Agent Abigail Borin to probe a double homicide aboard a research boat when an admiral's daughter becomes the prime suspect in the case. Meanwhile, LaSalle tracks down his estranged brother.

Guest starring: Eddie Matos, Kerry Cahill, Corbin Bernsen, Diane Neal

A Navy lieutenant commander and a friend of Pride seeks his help to solve his impending murder after he learns he has been poisoned with a lethal dose of radiation. CGIS agent Abigail Borin pairs up with the team again.

Guest starring: BD Wong, Russell Wong, Eyal Podell, Anne Dudek, Diane Neal

A fellow NCIS agent is shot dead while on security detail for a high-ranking Navy admiral. The team's investigation leads them to discover that the agent was the target due to a secret he knew about a sick child's biological father. Meanwhile, Brody's past is brought up by the security detail leader.

Guest starring: Ron Melendez, Scott Michael Campbell, Aarti Mann, Richard T. Jones

The stabbing death of a Mardi Gras partygoer leads the team to uncover a gang's plans for a major robbery at the height of the festival. Meanwhile, tensions rise between Pride and Laurel when he learns that she has been secretly visiting Pride's father in prison.

Guest starring: Yetide Badaki, Harold House Moore

When a Navy recruiter is killed in a hit-and-run, the team's investigation leads them to her two foster children and their recently returned father. Meanwhile, LaSalle gets concerned that Cade hasn't been showing much progress in his treatment.

Guest starring: Gillian Alexy, Christopher Meyer, Jon Eyez

Both LaSalle and Brody grow concerned with Pride's obsession with catching Baitfish, who is killing off many of his old associates and building a new empire.

After a Naval officer is found dead in a strip club, the team discovers that his death matches the MO of two unsolved murders, leading them to a mural with the names of unprosecuted killers. The list suggests that a vigilante may be at work. Meanwhile, Brody's ex-fiancé pays her a surprise visit.

In the morgue, Wade, Danny, and Sebastian are held hostage by a criminal who wants a secret that is inside a dead body, forcing Pride and the rest of the team into a desperate race against time to resolve the situation before an FBI team take charge.

A Navy commander's adopted baby daughter is kidnapped when he leaves her in the car while taking groceries inside, prompting the NCIS team to launch a search for the missing baby. CGIS agent Abigail Borin returns to help them with the case.

When Cade's girlfriend is discovered murdered in the back of his car, Cade is charged with her murder. NCIS joins in for LaSalle's sake, but he's ordered to stay off the case. However, an old enemy returns with a message for Pride with the episode ending with Baitfish aiming a gun at LaSalle's girlfriend.

In the aftermath of Savannah's murder and with the crime scene later being attacked resulting in the deaths of two officers and four more injured (as well as Brody who suffers a cut to her right arm), the team go into overdrive as all of New Orleans’ law enforcement searches for Baitfish. LaSalle seeks revenge for Savannah's death at Baitfish's hand. However, things get complicated when it's revealed Sasha and Baitfish have turned on each other and both are trying to get rid of the other.

Following a murder at the port in which a Navy officer dies after having his throat slit, Pride and the team investigate and discover that a dangerous West African terrorist has secretly infiltrated the city and is plotting an attack that could leave the entire population gravely ill with radiation poisoning.