The episode begins with Gibbs fishing. He imagines talking to his late mentor, Mike Franks. Mike takes out his gun and shoots into the water before disappearing. Gibbs sees dead bodies float around him and his team stands on the shore. Gibbs snaps out of his daydream as Parsons enters the conference room. Gibbs wants to know why he is being investigated. Parsons tells him that his actions have been inappropriate and now they are his responsibility. He says that the deaths of Jackie Vance and Eli David have opened doors to an investigation.
Parsons tells Gibbs that he is tired of watching Gibbs break the law. He tells Gibbs to step up and take responsibility, and he will leave his team alone. Parsons tells him that he wants the truth. Gibbs tells him that he wasn’t there. Tom Morrow is in Vance’s office. Vance asks Tom why Parsons is not going behind him. Tom explains that Parsons recognizes the political fallout of going after a man who has lost everything because of his agent’s poor judgment. So, Parsons is going for the next best thing; Gibbs. During the interrogation, Gibbs lawyer, Chegwidden, former advocate general, arrives. Vance called him. Gibbs and Chegwidden go way back. DCIS arrives and takes all the old NCIS case files. Gibbs calls McGee and tells his team to back off. Tony tells McGee to dig up dirt on Parsons.
In the lab, Abby takes out her aggression on a video game, with Parsons as target. Duckie and Palmer arrive and tell Abby that she needs to be very careful about what she says. They tell her that they found a listening device in the morgue. The Judge gives Chegwidden 48 hours to prepare a defense for Gibbs. The entire team meets in the elevator for a meeting. Palmer found another bug in the ladies room. Vance asks his team if they know about anything else that could hurt Gibbs. Ziva points out that there could be items at Gibbs’ house. Later, Gibbs arrives home with Chegwidden. He sees that his house has been tossed. He hears a noise and pulls out his gun. It is Ziva. Chegwidden tells Gibbs that they have to go to a safe house to talk. Gibbs takes them to a cabin that he built in the woods. They go inside when a helicopter circles overhead.
Later, at night, Chegwidden reads Parsons’ bio. McGee arrives with the body of the week. It is a dead Navy Seal in Virginia, Chad McBride. Gibbs tells his team to go and look into the case. They arrive at the crime scene. McGee tells Tony and Ziva that Chad’s wife, Emily, who is a flight attendant, came home to a box that was shipped from Riyadh. It had Chad McBride’s head in it. In the morgue, Duckie and Palmer examine Chad’s head. Palmer tells Duckie that he and his wife are adopting a baby. Palmer then checks the Geiger counter and he is shocked to see the scale. He tells Duckie that the radiation levels are really high. Duckie tells Palmer to suit up. The next day, Chegwidden wakes up Gibbs with a cup of coffee. Parsons meets Ziva in the elevator. He tells her that he is just doing his job. Ziva doesn’t say anything.
He tells her that he knows that she threw Bodnar off the ship and also killed her own brother, Ari. He tells her that she will be punished for these murders. Ziva simply walks out of the elevator. In MTAC, Vance talks to Captain Wayne, Chad’s Chief Officer. Wayne tells Vance that Chad was doing some top secret recon. He says that he cannot give more details about the mission. Vance tells Wayne that they have a radiation issue. Wayne goes silent a moment. He tells Vance to keep the remains secure while he speaks to his superiors. He tells Vance to keep this a secret. In the lab, Abby tells Tony and Vance that Chad was held somewhere in the Middle East and tortured. She tells them that he was beaten with a stick. Vance calls Tom. McGee finds some information on Parsons.
He tells Tony and Ziva that Parsons has secured tons of files that contain sensitive information belonging to high level justice department people. They figure out that Parsons is into blackmailing people. In the woods, CHEGWIDDEN wants to know about the people Gibbs and his team have killed. Gibbs tells him that he has no regrets. Parsons meets Vance in his office. He asks Vance about a missing file; the one with Abby’s results on a Mexican shooting. Vance tells him that he knows nothing about the file. In the cabin, the team tells Gibbs that Parsons is a first class blackmailer. They have enough information which can be submitted to the Inspector General. Gibbs tells them to stay out of this. Ziva tells him that this is about protecting her family. She storms out. Vance meets Tom. Tom tells him that there is a connection between Chad’s death and what is happening with his team.
Tom tells Vance that the CIA wanted Iran to believe that Mossad was responsible for Arash Kazmi’s death. He says that Bodnar did not kill Kazmi; the CIA killed him so that Bodnar would be the fall guy, and Iran and Israel would fight while US focused on domestic threats. Tom also tells Vance that Parsons doesn’t know anything about this. Vance asks him about Chad. Tom tells him that it is not good. Next, Gibbs arrives at his house. He imagines Frank accusing him of running away. He tells Gibbs to come clean and admit that there were good reasons for the things he did. The next day, Gibbs arrives at NCIS. His team is surprised to see him. He goes to meet Vance. Vance tells him about Kazmi’s death. Gibbs is not surprised. He tells Gibbs that Tom might have a solution and they could all get away with a clean slate, but there is a catch. It might kill Gibbs.
Later, Vance shreds the file on the Mexican shooting. McGee, Tony and Ziva agree to do what is necessary. Tony warns Ziva that she might not like how this ends. Ziva is fine with it. They go upstairs and resign, by turning in their badges. Back in the house, Gibbs takes out Frank’s files from a secret compartment and burns them one by one. The next day, Chegwidden, Wayne, Vance and Tom arrive to meet Parsons. They tell him that Gibbs is gone. Wayne tells him that Gibbs is on a special mission for JSOC, top priority. Tom gives Parsons a letter from the Inspector General, asking Parsons to postpone the investigation, effective immediately.
Vance tells Parsons that Gibbs’s team handed in their resignations, taking full responsibility for their actions. Parsons is shocked. He asks, “Is Agent Gibbs so valuable that you would allow this to happen?” Cut to four months later, in a dark room, Gibbs tries to stop Wayne’s bleeding. Wayne tells Gibbs to “do it”. Gibbs goes to the window and takes aim at someone getting out of a car. It is Agent Fornell. Gibbs pauses for a while and then takes aim again. The screen goes black and we hear a gun shot. The season ends.