The episode begins with some sailors training in a park. They see a Navy seaman chase a guy, and tackle him. They break up the fight. Someone, who is watching the whole scene on surveillance, decides not to intervene. Next, Ziva arrives at work in her new car. Tony asks her as to what she did with her Mini. She tells him that she sold it. Tony is upset because he really wanted to buy the Mini. Gibbs arrives and takes McGee with him to their latest crime scene. At the park, McGee tells Gibbs that the attacker is Petty Officer third class, Evan Lowry.
Lowry tells Gibbs that that man has been following him for a while, and when he confronted him, he ran. He adds that someone has been going through his emails as well. McGee and Gibbs are skeptical. Lowry is a cook on the ship, and he thinks that someone is trying to infect him so that the entire ship gets infected. McGee pulls out a GPS tracker from Lowry’s car. They now believe that Lowry is telling the truth. At NCIS, the team tries to figure out who could be following him. Tony tells Gibbs that Lowry was mugged two weeks ago, and all of this started after that attack. Ziva tells Gibbs that Lowry barely remembers the assault, because he got a concussion from a tire-iron to the head. Also, Lowry’s laptop and cell phone were stolen.
Gibbs tells McGee to trace the cell phone. He gets a hit. Richard Parsons, an officer from the Inspector General’s office, meets Vance to do some inquiry on Ilan Bodnar’s death. Vance is eager to get it over with. Parsons assures him that he will try to finish his investigation as soon as possible. He begins with McGee and Tony, who are staking out a complex, which was tracked down through Lowry’s phone. McGee intercepts a call being made from Lowry’s phone. They see a man walk out of the complex and manage to arrest him. In the interrogation room, the guy tells Gibbs that he found the phone in the trash. Lowry doesn’t remember if it is the guy who assaulted him. Gibbs asks the guy a few questions and figures out that the guy knows nothing. Abby finds the last page of some legal document from Lowry’s bag-pack, releasing them from any physical or mental trauma to Lowry.
Lowry's signature is on that document, but he has no idea what it is. In the morgue, Duckie tries to help Lowry remember when he signed the document. The time stamp on that document proves that he signed it few hours before he was mugged. Lowry doesn’t remember anything. The only thing he remembers is his best friend picking him up earlier that day. Jimmy tells him that the head injury could have affected his memory. Duckie tries another method. Since Lowry is a cook, Duckie tells him to try remembering the smell or sight from the day he signed the document. He tells Duckie that he remembers smelling bratwurst. Duckie tells him that the same blend was found in the recent morgue victim’s stomach. In the lab, Abby cooks various bratwursts and explains to Parson how she will test them.
Parson asks her about the memory card that she processed five months ago, which had the photo of the man who killed Tyler Wilkes, Eli David. Abby tells him that they didn't know who it was because the photos only showed the back of his head. She says that Ziva was the one who recognized that it was Eli David. Later, Gibbs takes Lowry to a bratwurst cart, but Lowry isn’t able to remember anything. Lowry then notices a warehouse and tells Gibbs hat he has been here before. Gibbs takes him to the warehouse. They see a guy Lowry remembers and he's eating bratwurst. Lowry tells Gibbs that he is the guy who was following him. A woman comes out of the office and tells Lowry to calm down. She tells Gibbs that Lowry is one of their test subjects. She explains to Gibbs and Lowry that the study is about examining the psychological effects of surveillance.
She tells Gibbs that they had volunteers, like Evan, who agreed to be watched, their mails be opened, etc. Gibbs asks her if they recorded the mugging. The woman tells him that they didn’t because the mugging happened a few hours after Evan signed up. They hadn’t started their surveillance yet. Lowry maintains that he doesn’t remember signing up. The woman tells Gibbs that Lowry’s ignorance made him the best test subject. Gibbs tells Lowry that he could press charges if he wants. The woman tells them that Lowry is being paid for the test; $1500. Lowry changes his mind on hearing about the money. The woman tells him that he was very excited when he signed up. At NCIS, Ziva tells Tony that Gibbs is not too happy about this study.
He wants them to look into the doctor who is conducting the study because a lot of Navy personal are being looked into. Parsons questions Ziva in the interrogation room. It looks like he is trying to make her uncomfortable. He wants to know why she waited for three hours before she told Gibbs that the guy in the photos, was her father. She tells him that she thought it was best to talk to her father first. He then asks her if she slept with her contact, Adam Eshel. He says that if she did, then it could be a threat to national security. Ziva tells him to go to hell. Tony barges into the room and tells Parsons that the interview is over.
Next, at the office, the team sees on the news that there was an explosion at the warehouse that was running the study Lowry signed up for. At the crime scene, Ziva admits to Tony that she slept with Adam when she went to Israel to bury her father. Tony tells Ziva that she must talk to legal. The team finds out that all the surveillance footage was destroyed in the blast, and the woman who was conducting the study, Dr. Hale, is at the hospital with minor burn injuries. Duckie calls Gibbs and tells him that they have a problem. Later, in the morgue, Duckie tells the team that Parsons is trying to dig dirt up on Ziva. Duckie shows her the picture of a young Schmiel, and tells her that Schmiel worked for the Israeli government in ’72, after the Munich killings. Duckie tells her that Parsons is questioning her loyalty to NCIS.
Later, McGee hacks into Parson’s files and comes across a locked filed from the Department of Justice. Parsons arrives at NCIS, and the team quickly gets back to work. They find out that a civilian, Simon Gravy, one of the test subjects, has disappeared. At MTAC, Tony and McGee watch Simon’s surveillance video. Ziva tries to get in but her retina scan failed. McGee tells her that her security clearance has been denied. Tony goes to inform Gibbs, but ends up following Parsons. Ziva tells McGee that Parsons has been accessing some of their old case files, including the ones before Ziva got there. In the elevator, Tony tells Parsons not to question Ziva’s loyalty. Parsons asks him what makes him think that he is going after Ziva.
Ziva figures out that there is only one person these files have in common; Vance. That means Parsons is going after Vance. They tell Vance, and Vance wonders why Parsons would do that. Gibbs explains that Parsons is trying to get Ziva to flip on Vance. Vance is slightly worried about Parsons. Tony tells them that he has bugged Parson’s phone. McGee arrives and tells them that he has tracked down Simon, and he is the suspected arsonist. In the interrogation room, Gibbs asks Simon if he was going somewhere because he emptied his bank accounts an hour ago. Simon tells him that he did not burn the warehouse. He says that he led a pathetic life and wanted a fresh start. He also says that he met someone who did not like being recorded.
He tells Gibbs that he is sure that no one from the study could have set the fire because no one was foolish enough to get into trouble, knowing that he was being followed by a camera crew. Gibbs states that someone who didn’t remember could have done this; Lowry. Next, Gibbs and Ziva arrive at a restaurant where Lowry is having lunch with a woman, Stella. Gibbs knows that Stella was a corporal. He tells Lowry that they ran a facial recognition on everyone Lowry came in contact with, during the study.
They know that Stella is UA. They know that Lowry set fire to the warehouse when he remembered about the study, so that he could destroy the surveillance with her in it. Lowry admits he set the fire because he was afraid that Stella could get caught. Lowry is arrested. Case closed. Stella tells Gibbs that she went AWOL because she did not want to continue after she had her baby. At NCIS, McGee listens to Parson make a phone call. He runs to Gibbs and tells him that they have a problem. He tells him that Parsons isn’t after Vance or Ziva. Before he could complete, Parsons arrives with some men. He knows that his phone has been bugged. He asks Gibbs if he would take full responsibility for his team’s actions. Gibbs asks, “What do you think?”. The episode ends.