On the first part of the NCIS crossover with NCIS: New Orleans, the team investigates when a plane from New Orleans carrying five people, including a man named Commander Lively, is unresponsive at air traffic requests as it flies over Washington. It appears all of the individuals in the plane are not alive and they have to figure out how to ground the plane.
Before getting the case, Tim and Tony discuss Tony’s breakup with his girlfriend, Zoe, before meeting Ellie in MTAC to be briefed on the case at hand. Images from the plane show the pilot and copilot appear to be dead, but they can’t get the plane on the ground. They find out the plane is owned by Blye Industries, a company that deals in technological supplies. At first, they believe there are just four possible deceased people on the plane.
Abby and Tim work together to figure out how to make the plane come down. She decides the best way to do it is hack into the GPS satellite to force the autopilot to realize it is going the wrong way. Just as they get the plane down, Gibbs gets a call from Pride with the flight manifest. It turns out Abby’s brother, Luca, was on the plane.
Abby desperately calls her brother and tells Gibbs she doesn’t feel that he is dead. Plus, he never told her he was coming to Washington and he doesn’t normally fly since he is just a chef.
The team goes to the crash site to find evidence and Tim goes inside, where he discovers the bodies of the pilot and co-pilot, an employee for Blye Industries, Commander Lively, and another male that is burned beyond recognition. However, he is wearing a chef’s jacket with Luca’s name.
Palmer and Ducky are waiting for Abby to come down and make an identification. Palmer wants to talk about the evidence he can see from the bodies, but Ducky wants to wait until they can do the autopsies. Abby comes down with a list of things she compiled about her brother’s identifying features. As Ducky opens the drawer where the body is, Abby can immediately see from the person’s earlobes that it is not her brother. He is still alive, but missing.
In New Orleans, LaSalle and Percy are searching Luca’s home while talking to Tony over the phone. LaSalle finds evidence while Percy inquires as to how she knows Tony’s name. It turns out she knew Zoe. LaSalle shows Percy a bag that has cash, weapons, and a listening device.
Gibbs and McGee are investigating and discover that Commander Lively had a meeting with the Secretary of Defense scheduled once the plane landed in Washington. They need to find out why he had to meet with SecDef and Abby comes in to tell them she got a text for help from Luca and how to find him.
In North Carolina at an amusement park, Abby and Tony arrive to try and find Luca. It is difficult, at first, since they have to use clues left by the young man to try and discover his whereabouts.
Tim is having a hard time with Major Mass Spec, but he is able to tell Gibbs that no prints were found on the bug in Luca’s house but there was a second one in his home.
Leon and Gibbs discuss the case and they learn Jenner, who is still not returning calls, has been avoiding calls from the Secretary of Defense. Gibbs will have to go find him.
Abby and Tony find another clue, this time it is a hippo, and it leads them to another area of the park that used to have a haunted house.
Gibbs and Ellie meet with Blye CFO Dalton Greenbrick and Blake Huxley, Head of Security at Blye, to ask to speak with Jenner. While Dalton tries to stall, Blake admits that Jenner is missing.
Tim is finally able to get the mass spec to work and tells Gibbs the poison was batrachotoxin. The poison was found on silverware the passengers on the plane handle. They got security footage from the plane in an attempt to find out who was handling poisoned silverware that was used to make the passengers on the plane sick. It shows a photo of Luca.
As Luca reunites with Abby and tells her he doesn’t remember anything that happened and he woke up confused in a hotel, Tony gets the call from Gibbs. After getting a call from Gibbs, Tony has to arrest Luca.
Tim and Ellie discuss the case. They know Commander Lively had a meeting with Jenner Blye before flying to Washington to see the Secretary of Defense about something to do with national security. Blye’s car was found in a river but he is still missing. Abby comes in and asks them who is interrogating her brother.
When she finds out it is Gibbs, Abby goes to him to defend her brother. She listens in on the interview, but when Luca says he needs a lawyer, a furious Abby comes over to deal with him herself. They learn he works for Blye as a chef, but doesn’t know anything about his business dealings or anything about the crash. She knows he didn’t do anything wrong, but thinks he might be protecting someone. Using sign language, she determines a woman is involved.
Abby tells the entire team about how her brother sees only the good in people and can be naïve. He is seeing a girl named Eva, who refuses to have her photo taken and hasn’t told him her last name. Despite this, Luca is sure she is a good person.
Brody and Percy tease Tony from MTAC as they sweep Luca’s house. They are unable to find any prints, but then they spot a caricature photo that shows Luca with an unknown woman. Abby is able to use the sketch to minimize the exaggerated features of the woman. After plugging it into her search, she discovers the woman is wanted in five agencies, including their own.
Leon and Gibbs show Abby and Luca that she is Eva Azarova, who works for their old “friend,” Pavlenko. Despite this, Luca still believes she is good since he thinks that Pavlenko has helped them before even though it was done for his own needs. Luca gets a call on his phone and it turns out to be Eva, who wants to talk to Gibbs.
While Gibbs is on the phone with Eva, Abby tries to narrow down her location. Even though Eva hangs up before she can get a detailed view, she is able to determine it came from an area on K street and Luca recognizes that a Russian hotel is in that area.
Tony and Gibbs go to the hotel, only to find Pavlenko and learn Eva is actually in New Orleans. He informs Tony and Gibbs that a Russian operative was the one who took Luca’s place on the plane and he had sent him there in his stead. He had information on project Manta Ray, which was something the Russians were trying to steal from the US. This was likely the information the Commander wanted to talk to SecDef about. As he talks, he opens a bottle of wine and begins to drink. He offers the bottle to Gibbs, who declines.
Before Pavlenko can say more, he begins convulsing and dies. The team comes and they learn the poison was found on the cap and Tony realizes Gibbs touched the bottle. Luckily, his hand wasn’t near the cap. Even though a Russian consulate is on its way for the body, Gibbs tells Tony they still need it.
Abby and Luca talk in a diner and he tells her he is going home. She is worried, though, that someone may still be after him.
Pride and Gibbs talk on the phone about bringing Pavlenko’s body to New Orleans. We see Ducky and Palmer on the road, but then a Russian diplomatic car stops them and men get out with their guns drawn.