When a private jet headed from New Orleans to Washington, D.C., goes silent for more than 30 minutes, fighter jets are sent to shoot it down if there is no sign of life. When all aboard are determined to be dead, the jets are within seconds of doing so when Abby figures out how to make the plane crash itself. This is helpful because it will preserve more of the evidence needed to figure out what happened.
The plane belongs to Jenner Blye, a Tony Stark-type of inventive genius, who has had dealings with the Department of Defense. The shocking news is that all aboard have been poisoned, including Commander Lively who was on his way to D.C. for a meeting with the Secretary of Defense.
Abby's brother Luca (guest star Tyler Ritter) becomes the main suspect, especially when it is determined that poison was involved and Luca was the chef responsible for the food. The bodies are taken to autopsy, including the one wearing the Chef Luca coat, but Abby takes one look and is able to determine it is not her brother: the ears are wrong.
Because of Luca's involvement and disappearance, his apartment is searched by the New Orleans NCIS team and Lasalle discovers a false wall, behind which is hidden a bag with ten grand, two 9mm guns, and a listening device.
Meanwhile, Abby gets a coded text from her brother, so DiNozzo drives her to the secret meeting place: the Colossal Fun Amusement Park in Redbird Bolt, N.C., where, after following some cryptic clues, they find Luca.
In her absence, McGee is playing Abby and working with the mass spectrometer to figure out what poison was used and how. He discovers the poison is from a South American poison dart frog that is lethal to the touch, and someone put it on the utensils. Then a photo of Luca with the silverware is found and DiNozzo has to arrest him.
Bishop and Gibbs head to Blye Industries, but the chief of security is not very helpful. It turns out Jenner Blye is missing and they are trying to cover it up – until his car is found in the river in New Orleans – but still no body.
With Luca in custody, Gibbs tries to interrogate him, but he asks for a lawyer. Abby, convinced of his innocence, tells him to talk. She interviews him, figuring there is a woman involved. He is always a sucker for a woman with a sad story.
Luca admits he met Eva at a church prayer group. He is helping her because she is running from her ex. He also tells his sis that he woke up in a strange motel room and he had been drugged. His alibi holds. The owner of the motel saw him.
Another search of Luca's apartment turns up no fingerprints or DNA evidence of this woman Eva, but a sketch. Abby uses the sketch to run a facial recognition search. Eva is in four databases. She is a Russian sleeper agent.
Luca gets a call from Eva, who asks to speak with Gibbs. They track her to a Russian restaurant on K Street. Gibbs and DiNozzo don't find Eva, but her boss: Russian attaché Anton Pavlenko, who tells them he is helping them at the risk of his life. He explains the man who took Luca's place was going to represent him at the meeting with the Secretary of Defense. Russia was planning to steal technology from Blye, who developed a next-generation warship undetectable by radar for the U.S. government. The theft could start a war. When Pavlenko downs his vodka, he dies. It was poisoned using the same neurotoxin.
Gibbs whisks away Pavelenko's body and has Ducky and Palmer drive it to New Orleans for autopsy, so the Russians can't get it. On the way, they are intercepted by a van with Russian consul plates and held at gunpoint.
"Sister City: Part Two" on "NCIS: New Orleans"
It turns out Ducky and Palmer don't have Pavelenko's body. Bishop does and she delivers it to Loretta, the medical examiner, in New Orleans.
Luca, now back in New Orleans, is trailed by Pride, who finds him in a restaurant. He lies that Eva isn't there, but then she shows up. When she refuses to go with Pride, and pulls a gun, Luca helps her escape, making him look guilty all over again.
Pride tries to tell Luca that Eva is bad news, but he won't listen. Luca says Eva may not be everything she claimed to be, but she is good inside. He won't help Pride trap her. Pride puts Luca under house arrest at NCIS headquarters to keep him safe.
Loretta discovers that Pavlenko's death was caused by the same neurotoxin as the people on the jet. Sebastian is able to use blood from the mosquito bites on Pavlenko's body to determine where he had been. The location was the wetlands, 100 miles outside of New Orleans. It's a turtle preserve, where Pride and Lasalle find Blye hiding out in the monitoring station.
Blye says he knows exactly what kind of danger he is in. He has water and food. He will stay there until they sort it out. He takes a swig of water and is poisoned. Pride and Lasalle manage to save his life.
Blye tells them the DOD gave his company approval to build a version of the next-generation ship – without the military weaponry – and they sold one to the Norwegians. But now it turns out, the Russians had tricked Blye Industries and they had the ship.
Sebastian accidentally discovers a transmitter in Pavlenko's body, and the NCIS team realizes that the Russians have heard everything. They still think it is Eva, but when they track down the signal, it leads them to Paulina Kurteva, a former GRU agent who knows Pride and claims she works in the diplomatic core now.
Pride syncs his phone with one of the Russians, and they follow them to Eva Azarov, who still looks like the main suspect. Shots are fired. The Russian bodyguards are dead, and Paulina is in the closet.
It is looking bad for Eva, and Sonja tells Luca that Eva is wanted by NCIS and the Russians. There is nothing he can do for her now.
Even so, Luca breaks out of NCIS and goes to meet Eva. Pride is able to track Eva because she, like Pavelneko, has a transmitter in her teeth and Paulina gave him the code.
Eva tells Luca that she wants to apologize. She had Luca come to her because someone is tracking him. At first we think it is Pride, who shows up, but then shots are fired from the balcony. Eva goes after the shooter, putting her life in jeopardy. Pride is not too far behind.
The mystery shooter is Blake Huxley, Blye's security chief. He was trying to kill Luca because he was present at the meeting at Jenner Blye's house with Commander Lively and he might have overheard something he shouldn't have.
It turns out Jenner Blye is guilty of treason. He is arrested as he is getting on a jet to Venezuela. He also poisoned himself to throw NCIS off the track, which is why he didn't die.
Eva thanks Luca for believing in her. She kisses him and leaves for Washington, D.C., where she will be deposed.
Luca calls Abby to let her know he is okay. Vance mentions that the ship the Russians stole is about to hit an "iceberg."
On the personal side, DiNozzo and Zoe Keates broke up. He claims it was amiable. Bishop and Jake are divorcing, and Bishop is okay with it. And Gibbs cut his hair again, saying, "I don't need it anymore."