Gibbs arrives at William Decker's diner, where Tony and Ziva are collecting evidence. After Gibbs informed the Secretary of the Navy of Jenny Shepard's death, the Secretary sent NCIS Assistant Director Leon Vance to process the crime scene.
Inside, Vance describes the gun battle to Gibbs. Jenny had faced five shooters, but only four bodies were found. There were also four .45 caliber shell casings, but no matching weapon. The fifth shooter escaped in a car parked behind the diner, leaving only a tire track. Vance receives a call ordering that the news of Shepard's death is to be kept quiet. He then departs to accompany the bodies back to Washington, where Ducky will perform the autopsies. Gibbs puts Tony in charge of the scene, and leaves.
Gibbs meets up with Mike Franks and alerts the latter that Vance knows someone else was at the diner. Franks tells Gibbs everything, beginning with Shepard calling him two days ago, and ending with his being outside behind the diner when the four shooters attacked. Franks killed two of them as they entered through the side door. But he was too late to stop the others, who entered through the front door and confronted Shepard inside. All Franks could do was put an extra shot into those men, to ensure they were dead.
Like Shepard, Gibbs says that they had gotten away clean after the European operation nine years ago. They had been sent to Paris to eliminate two people, one kill each. Gibbs disposed of his target. When Franks asks if he'd verified Shepard's kill, Gibbs replies, "Jen was a pro." Franks insists that Decker and Shepard had known something Gibbs didn't, and gives him the number of Decker's "insurance policy". Because the person who sent hired gun Viggo Drantyev is still out there, Franks wants to stay and help. Gibbs urges him to return home to Mexico before Vance can find him.
Meanwhile, Abby and McGee identify the tire track found behind the diner. The tire is a custom mold, sold exclusively to a specific car rental chain for their Mercury Grand Marquis vehicles. At Tony's order, they check the agency's most recent Marquis rentals at their Los Angeles International Airport location. Only one rental is outstanding, to a Joe Hill from New Mexico. Hill isn't listed with the state's Department of Motor Vehicles, so the driver license he presented must be a phony.
Gibbs calls McGee, gives him Decker's mystery number, and orders him to find out what it is. While the two are talking, McGee receives a copy of Joe Hill's driver license from the car rental agency. To McGee's surprise, "Hill's" photo is of Mike Franks, and Gibbs knows it. Despite Vance's wanting that information, Gibbs orders McGee to erase the file.
Vance arrives back at NCIS headquarters while McGee is processing crime scene photos sent by Tony. Three of the four shooters were Los Angeles felons hired strictly for the job. The fourth is Viggo Drantyev. McGee tells Vance that Drantyev, whom Shepard saw at Decker's funeral, had traveled to Los Angeles by way of Washington. Vance orders McGee to have Washington Dulles Airport send over all their security video footage of Drantyev's arrival.
The airport video footage shows Drantyev passing through customs and the terminal, then outside where he hailed a taxi. A few moments later, a woman got into the taxi with him. Since professional killers don't share cabs, the two must have known each other. The woman at the airport could be the woman Shepard photographed in the SUV at Decker's funeral. Tony and Ziva don't recognize her. Vance then addresses Gibbs, but the latter is gone and his cell phone is on his desk.
McGee finally identifies Decker's mystery number as an NIS (Naval Investigative Service) case file number. Decker hid his insurance policy in plain sight, in one of his old case files. With Ziva and Tony in tow, Vance goes to the agency's storage annex and finds that the file is gone. The file clerk admits that his old friend Mike Franks was there an hour before, and he had briefly left Franks alone with the file. Vance asks Tony and Ziva why Franks took Decker's insurance policy. Ziva replies, "Honor. He fulfills his debt to Director Shepard. He disappears with the file. It ends."
Abby and McGee identify Drantyev's travel companion as Natasha Lenkov. She's a citizen of Uzbekistan who owns a successful import/export business. However, she didn't exist prior to 1999. Whoever she was before, she is now Natasha Lenkov.
Armed with Drantyev's cell phone taken from Abby's lab, Gibbs goes to Shepard's home and sits down in the study to wait. Vance calls and asks him for Natasha Lenkov's real name. Gibbs answers, "Svetlana Chernitskaya." She had been the handler for former KGB assassin Anatoly Zukov, who sold his services to the highest bidder after the Cold War ended. He disappeared in 1999, the same year that Natasha Lenkov appeared out of nowhere.
While Gibbs and Vance are talking, Gibbs puts Vance on hold to take an incoming call from "Natasha". Gibbs tells Lenkov that Drantyev is dead, and says he needs her to come see him. She demands to know who he is, and he replies, "Mr. Oshimaida." During that conversation, McGee traces Drantyev's cell phone signal to Shepard's home. Vance orders the others to stay put, then heads out the door.
Gibbs is standing at the liquor cabinet with his back to the door, when Lenkov enters with a gun pointed at him. She and Anatoly Zukov had been partners in love as well as in crime. It had taken her until now to locate Decker, Shepard and Gibbs. In 1999 Gibbs had killed Zukov, as assigned. However, Shepard had failed to eliminate Chernitskaya/Lenkov because when the time came, Shepard couldn't bring herself to pull the trigger.
Lenkov is about to shoot Gibbs, when she is brought down by Mike Franks. When Franks expresses surprise that Shepard had faltered in Paris, Gibbs explains that back then she wasn't the woman of steel who fought to the finish in the diner. Franks says it'll be Gibbs' neck when Lenkov's body is found. Gibbs replies, "They're not going to find her body."
A short time later, Gibbs and Franks stroll along the sidewalk as fire crews arrive to find Shepard's home engulfed in flames. Vance catches up with them and asks Franks what is in Decker's insurance policy. Franks replies, "You can read it for yourself. I'll leave it for you in my will." As Franks leaves, Vance asks Gibbs what to tell the Secretary of the Navy. Gibbs replies, "Anything you want."
The official story is that Jenny Shepard died in a fire, caused by a pilot light igniting leaking gas in her home. Leon Vance is appointed to succeed her as NCIS Director. In his new office he opens a locked drawer, takes a page from his own agency personnel file, and puts it down the shredder. He then calls in the team, and pulls three other personnel files from his briefcase. The Mossad liaison position is being terminated; Ziva is going home. McGee is being moved to the Cyber Crimes Unit. Tony is being reassigned, as Agent Afloat aboard the USS Ronald Reagan. Finally turning to Gibbs, Vance hands him the three files and says, "Meet your new team."