Four months ago, Richard Parsons arrives at a fancy hotel and wants to talk with Tom Morrow and Secretary Jarvis about NCIS. Tom says this isn't the place to talk about that but Richard says his job is to clean up the NCIS but he has been sidelined by some half-assed mission because they want Gibbs' to play cowboy. Tom says that Homeland isn't the only organization authorizing this. Richard says it is wrong that Gibbs was given the mission. Richard asks what the one mission is that can trump a career of rule breaking. Tom says there is a line in the sand and warns Richard not to cross it. Tom goes back into the hotel and Richard walks away. An explosion rocks the building and throws Richard to the ground.
Back at NCIS headquarters, a TV news report states that the Secretary of the Navy, Clayton Jarvis, died in the explosion. Abby complains to Mallard that if Richard had not been around then maybe Gibbs could have been here to stop it. Abby asks why they didn't do more to stop Richard's investigation. Mallard says they must stop feeling sorry for themselves. Those who have died are counting on them to solve the investigation. Gibbs walks into the office to meet with Captain Wayne and Leon Vance. Leon Vance receives word that Tom Morrow has been rushed into surgery and may lose his legs. Washington wants answers and Vance thinks this may have just been the warning shot. He suspects that the bomb may be related to McBride's murder. They tell Gibbs to find McBride's killer and find out how it relates to the bomb.
Tony receives a wake-up message from Ziva. The two of them chat online while she is on a bus to Tel Aviv. He asks if she wants some company and she says yes. He tells her to count to a million and orders a plane ticket to Tel Aviv.
Delilah meets Timothy in a restaurant. She tells him that the device used in the bomb blast wasn't Middle Eastern but American. Abby is on her way out and tells Tim that Gibbs is leaving town. Delilah comments how awkward their meeting was but Tim is too busy thinking of where Gibbs could be going.
Vance tells Gibbs that the president will be calling Jarvis' widow today but he wanted to get there first. Gibbs and Vance agree that he was a good boss and Vance says he was an even better friend. Vance is worried about Gibbs' trip and considers grounding him. He tells Gibbs to be careful in Tehran.
Gibbs walks through the streets of Tehran and watches some men. They point at him and he looks around him. He pulls his gun out and looks for a suspicious man. The man starts firing at Gibbs but he is taken down by some men that Richard has hired. Richard says that he knew when they got Jarvis, Gibbs was next. Richard is here to save his life. Gibbs' informant didn't show and Richard says his team knows too much. He thinks NCIS is being set up. Richard believes that Gibbs was sent to Tehran not to investigate McBride's death but to separate Gibbs from his team. The two men plan to meet Lt. Kagen, one of McBride's coworkers. Gibbs doesn't understand Richard and Richard says that sometimes people do the wrong thing for the right reason.
Mallard delivers lunch to Mr. Palmer in the morgue but finds another man instead. The man punches Mallard and tackles Palmer to the ground. Palmer yells for security but Mallard knocks the unknown man out with a bowl.
Gibbs and Richard ask Kagen about McBride. He says his death is classified and lies at first. Kagen knew that McBride was headed home but didn't actually see him board the plane home.
Tony prepares to leave for the airport and texts Ziva. While reading a message he notices a laser dot on his chest. He jumps out of the way as bullets shoot in through the window. He takes cover and pulls his gun out.
Vance pours a drink for Tony and asks about the shooter. Tony is supposed to lay low and he comments that he can't lay much lower than staying at home. They have a man in custody who was snooping around in the morgue. Tony asks Vance if he can just stick around NCIS headquarters as a visitor and Vance says they could use the company.
Vance interrogates the man, Vincent Cheng, and asks who he works for. Cheng doesn't know and says that he was just given money to access the NCIS database. Vance leaves the interrogation when he receives a phone call from Gibbs. Vance is surprised to see Gibbs working with Richard. They state that McBride's mission didn't exist and he was just a decoy. They believe that he returned to the US alive and someone made it look like the Iranians killed him.
Tony wakes up in a seat at NCIS and thinks he's in a dream. Murray and Palmer explain to him the details surrounding Cheng and his firing from the FBI. Murray says that someone has been trying to access their system from the outside but the only thing they have been able to access is old employee records. Tony calls Timothy to warn him that his cell is being tracked. Timothy throws his phone out and goes to get a cab. He is stopped by two black cars though and Agent Fornell forces him into the car. He radios in that they have Timothy and are bringing him in.
Timothy is taken to an apartment where Tony and Vance are already waiting for him. Vance says that Gibbs walked into a trap and Tony was almost killed. Fornell fills them in on a young extremist who may be responsible for killings and started a new terrorist cell. He has been brokering deals between terrorists and American companies. Vance asks why NCIS would be targeted and Fornell says because they think they won't play ball. Vance asks if Homeland knows about this and Fornell says they have known since day one.
Vance visits Tom Morrow in his hospital room. He asks if he knew about the terrorists who have dealings with the companies. Tom says he would never condone an attack and he was almost killed by them. Tom tells Vance that Ziva is the next target.
Gibbs returns to the office and asks what is going on. Tony answers but Gibbs already knows everything he tells him. Richard is with him and apologizes about the earlier misunderstandings. Tony and Timothy both say they want their badges back and he agrees to get them back. He tells the team that McBride was set up and killed in a way that made it look like Iranians did it.
Gibbs asks Abby for the test results but she doesn't want to go near Richard. She ran the sand grains found in McBride's hair and finds some sand from a desert in the US. Abby believes that McBride was murdered and beheaded in Arizona.
Tony calls Adam and asks him to track down Ziva without alerting anyone else to the fact that he is looking for her. The NCIS team looks into McBride's commanding officer to see if he was the one who sent McBride to the middle east.
Captain Wayne is visited at home by Gibbs and Fornell. They have a letter that states that Wayne changed McBride's orders, the orders that led to his death. Wayne didn't know that McBride would be killed. He was blackmailed into changing the orders. Wayne says he will resign and confess to everything. Gibbs says he will serve time in prison.
Vance introduces Gibbs to Mendez, who works with the public anti-terrorism coalition. He is there because he was working with Homeland when they were investigating the terrorist they are looking for. Gibbs asks if Mendez has any property in Arizona. They think there may be a terrorist cell there.
Tony and Richard ride in the elevator together and Richard offers Tony a peace offering. It's a safehouse that Ziva could be hiding at.
Gibbs asks Fornell how long he knew NCIS was in trouble before he contacted them. He says right away and Gibbs says that no matter how the whole thing turns out, he has Fornell's back.
Back at NCIS, Abby, Mallard and Tim have found that the bomb was in the tubing of a bike and they have tracked down a group of people who makes bombs like this. They are located in Yuma, Arizona.
A team of FBI agents led by Gibbs enters an empty house in Yuma. There are handcuffs with blood on the ground and pictures of the NCIS team and targets on the wall. Gibbs finds Mendez and says he needs to get him somewhere safe.
Adam enters a house with a team of men and finds many bodies. He tells Tony that Ziva was there because she left a necklace on a picture frame.
Back at home, Tony looks at an old picture of himself and Ziva. He wonders to himself where Ziva could be.