The episode begins with a young Ziva praying with her family. Cut to present day, her praying in a synagogue, asking God why she should still have faith. Tony arrives. He wants to be anything she would want him to be. She tells him she does not want sympathy. She wants revenge. At NCIS, Jarvis gets 48 hours from the Secretary of State before they tell Israel what happened. They caught the shooter, but not the ones who hired him. Jarvis is angry that no one told him Eli David was in the country. Gibbs tells him that there was nothing much to tell.
He was in the country for a day and the next day he was killed. Gibbs then learns that Deputy Director Craig is on his way back to fill in for Vance. In the morgue, Duckie puts Jackie Vance away. She died of a single gunshot wound. Gibbs asks Duckie if he is fine; but Duckie evades the question. He says that the shooter committed suicide by cyanide, but they haven't IDed him. But the cyanide only expedited the inevitable; the man had only six months to live as he had liver cancer and looks like he wasn’t being treated. Vance comes into the office to find Deputy Director Jerome Craig in his chair. He was buying chocolates for Jackie in Geneva when he got the news. He excuses himself. Jarvis asks Craig to give them a minute. Vance asks to be part of the investigation.
Jarvis will keep him in the loop, but says he can't be involved. Outside, Craig assures Gibbs he is not interested in Vance's job permanently. Gibbs assures him he has his back. McGee IDs the shooter as Roland Ames, a Swedish mercenary. Gibbs wants them to track down Roland’s dependants who he could have dropped the money to. But first he wants Gibbs to track Eli's Iranian friend, Kazmi. Gibbs dropped a bug that McGee gave him a while back in Kazmi’s pocket. It is a remote tracking device. They track him to Georgetown. Down in the lab, Abby makes cookies. Ziva drops by. She tells her that she wants to see her father’s body in the morgue. Abby tells her that it is a giant secret and the news of Eli’s death cannot leak out.
Ziva knows she has to pretend her father is still alive. Ziva wants to know about the bullets, but Abby says she can't tell her. Gibbs walks up to Kazmi on the street. Gibbs pulls him into an alley and pulls a gun on him, demanding to know where Eli is. Kazmi doesn't know. Gibbs takes him in to NCIS to break the news. Kazmi says he approached Eli about forging peace. He couldn’t have possibly killed him. To prove his innocence, he can provide intelligence on all the possible suspects. He says that Eli had a lot of enemies and so did he. Eli’s death could only mean that he is up next. In MTAC, McGee chats with Gavriela Adel, their mole in Jerusalem, who has heard from her contacts that Eli David was going to visit Ziva.
She says the First Wave group, a pro-Palestinian organization funded by an American billionaire named Gustafson, was out to get Eli David. Back in the office, McGee finds a wire transfer of $3 million to the Roland’s ex wife just after the shooting. Tony interviews Gustafson about First Wave. He admits contributing because of his oil ties in the Middle East. Gustafson is about to call his lawyer when Vance busts in, full of rage, and asks Gustafson what he thinks about collateral damage to innocent people. Craig diplomatically gets Vance out of the room, and then asks him, on Jarvis' behalf, to take administrative leave. Vance agrees. Duckie finds Ziva in the dark morgue standing outside the drawer that holds her father. She wants to take his body to Israel for burial according to Jewish custom.
Duckie agrees to help, despite the secret murder investigation. Tony and Gibbs come down, telling her to go stay at Tony's because her place isn't safe. At Tony's, she sees that he has brought in her old friend Schmiel for her to talk to. Ziva is glad to see him and she thanks Tony. Back at NCIS, Mossad Deputy Director Ilan Bodnar comes looking for Ziva and Eli. He demands they call Jarvis. They call Gibbs instead. At Tony's place in the middle of the night, he hears Ziva making troubled noises in her sleep. Back at NCIS, Craig briefs Bodnar on Jackie and Eli's deaths. He assumes the Palestinians or Iranians are behind it. Craig tells him the Israelis have agreed to let NCIS lead the investigation and the Israelis get to prosecute.
Bodnar doesn't agree to cooperate. Gibbs meets Vance. He can't even tell his kids who killed her. Vance tells Gibbs he now understands some of what Gibbs’ choices of getting revenge for his wife's murder. He asks if it was worth it, but Gibbs doesn't answer. Vance asks Gibbs to catch whoever did it to keep war from breaking out. At Tony's place, Ziva checks her email and learns Bodnar is in town. She is upset that Bodnar knows about the death and she is not kept in the loop. At NCIS, Abby finds the bullets were Russian, from a batch seized by Swedish police last year. They were smuggled by an Iranian named Omeed Abasi. He is an Iranian arms dealer. He is not in the Iranian intelligence files Kazmi gave them.
Gibbs talks to Kazmi, who knows Omeed's name and is surprised he wasn't in the intel files. Craig and Gibbs believe him and don't think Kazmi's involved. Bodnar drops by, angry over having learned that they believe Kazmi really wanted peace. He thinks Kazmi and Iran are responsible and says it could lead to war. At Tony's place, Ziva sees an incoming video call on Tony's computer and answers. It's Bodnar, he wants to see her. When she says no, he says he'll just track her down. Kazmi checks with his office and finds Omeed was in the files they sent but there was a six hour lag from when they sent the files and when they arrived. They were hacked.
McGee tracks the wire transfer to Roland’s ex-wife to a bank account in the Caymans labeled Virtue. They call Ziva to ask if the word “virtue” reminds her of anything; like a family name or something in a different language. She tells them that Virtue is "Tohar" in Hebrew; Ilan Bodnar's middle name. He's on his way to see her. The team leaves for Tony’s apartment. Tony tells her where to find the gun taped to the back of his toilet. Gibbs and Tony arrive there first. McGee reports Bodnar isn't at his hotel room.
Ziva thinks that he could be watching them. Jarvis, Craig and Gibbs brief Kazmi on the fact Bodnar is behind Eli's death, trying to frame Iran and take over as director of Mossad. Gibbs commends him for trying to forge peace. Kazmi gets a ride to the airport in an SUV. When his car stops on the street, it explodes. Next, Ziva and Schmiel prepare to fly with Eli David's body to Israel. Tony arrives to see her off. She gives him a hug. He whispers something in her ear in Hebrew. "I know," she says. The team is at Jackie’s funeral. Leon consoles his children. In Jerusalem, Ziva leaves a prayer in the wailing wall. Ziva then plants a small tree. The episode ends.