Navy Petty Officer Kyle Friedgen is set free from a murder trial due to mishandling of DNA evidence.
Carrie Clark, a defense attorney who we met in NCIS Season 11 Episode 8 (entitled "Alibi"), meets with Gibbs at a diner, to ask him for a favor. Kyle Friedgen sits down and tells Gibbs that his wife has left him and his shipmates are harassing him because they all think he's guilty of murder but got off on a technicality. He asks Gibbs to arrest him so he can be court-martialed, so the truth can come out in court.
Gibbs tells them that JAG agrees to charge him with murder, pending the results of the NCIS investigation.
In reviewing Friedgen's life, the NCIS team discovers he got his girlfriend Joy Vanatter pregnant at age 16 and was arrested for domestic abuse after they got into a violent argument.
Since then he has straightened his life out but Vanatter turned to drugs and prostitution.
Kyle was charged with her murder.
Tony and McGee head to Baltimore to find out what the police know about the murder investigation.
Clark tells Gibbs that the DNA that was ruled inadmissible as evidence was a syringe containing some of Vanatter's blood, which was found in Kyle's car.
Kyle tells Gibbs he hadn't seen Vanatter in years. On the day of her murder, she had texted him, saying that she wanted to meet with him. He says he didn't.
Detective Malone reveals that the cause of Vanatter's death was blunt force trauma, and that her body was moved post-mortem.
State Attorney Alan Wyner tells McGee and Tony that the warrant to search the car wasn't signed until a few hours after he'd advised detectives to begin the search. He tells them it was a misunderstanding between him and the judge's clerk.
Tony and McGee interview a former informant named "Cheech" about Vanatter. He tells them Vanatter had stopped hooking to buy her heroin, and that she had hooked up with a businessman who was into S&M.
Abby traces the money found on Vanatter's body to a bank machine, where it had been withdrawn by Friedgen. He had given her the money, despite having told everyone he hadn't seen her in years.
Gibbs questions Friedgen, who admits to having met her to give her the money. Friedgen tells him that Vanatter had threatened to tell Friedgen's wife about their past together, which is why he finally agreed to meet and give her the money. He tells Gibbs he didn't tell the police about that meeting because he panicked.
Gibbs tells him he's putting Friedgen in custody for the night, and will charge him with murder in the morning.
Ducky and Abby determine that the heroin found in Vanatter's body doesn't match the low grade heroin found in the syringe, proving that Friedgen's claim that the syringe was planted may be true.
Bishop and Tony go back to Baltimore to investigate the last drug charge placed against Vanatter two years ago. They open the evidence box and find a needle that was supposed to have been found in Vanatter's arm. They note that the evidence box had been accessed three weeks ago by Assistant State Attorney Alan Wyner.
Abby discovers that the needle in the evidence box had never been used. Wyner had switched out the needles in order to implicate Friedgen in Vanatter's murder.
Gibbs, Tony and Marone arrest Wyner for the murder of Vanatter. Turns out she was blackmailing him about his S&M activities. He murdered her and then pointed the evidence to Friedgen. He then deliberately messed up the evidence so that Friedgen couldn't be convicted.
The other story in this episode involves Jake and Bishop.
Jake tells Bishop that he's suspected of knowing about the threat assessment prior to the conference in Dubai, and of using that knowledge to make sure he was elsewhere when the bomb went off.
Jake tells Bishop he goes to the same restaurant the both of them used to go, every day. She decides to surprise him at the restaurant, only to find him sitting at a table with a woman named Taylor Matthews.
Bishop gets Abby to pull up the tape of the taxi cab video she'd viewed when she was worried about Jake being in the explosion in Dubai. The person in the cab with him was Taylor Matthews, a member of NSA's Internal Affairs.
Bishop pays a visit to Gibbs at his home after midnight. She tells him what's on her mind, about Jake possibly coming under NSA investigation for being the leak in the agency.
Jake admits to Bishop that he's been having an affair with Taylor.
Bishop leaves a note for Jake, telling him she's going home to Oklahoma and that she's not sure when she'll be back. She tells him not to contact her.