A civilian is killed during a Marine practice bombing run over a dumping ground for old cars and scrap metal. The Marines saw him in the target area too late to stop the bomb drop. Gibbs and team meet Gunnery Sergeant De Luca of the Army Criminal Investigative Division, whose treating the scene as an accidental death. De Luca's initial theory that the bombing victim was a scavenger, this is disproved by the man's expensive Italian shoes.
Kate wonders how the victim got there in the first place, as the nearest civilian road is at least five miles away. Gibbs follows the victim's footprint trail back to one of the junked cars. Inside the car is a second, incinerated corpse. The bombing victim's death was no accident.
Ducky determines that the bombing victim's facial injuries were caused by a brutal beating before he died. The burned victim died at least six months ago. Someone has been using the bombing range as a bone yard for dumping bodies.
From the AFIS database, Abby identifies the bombing victim as career criminal Victor Gera. As she and McGee review his record, an intruder hacks into Abby's computer. Gibbs and Tony enter the lab as Abby and McGee frantically try to stop the attack. Gibbs solves the problem by unplugging the computer's power cord.
Abby sets up her computer to trace the hacker if he tries to access her machine again. He does, and she traces him only to be totally dismayed at who it is. McGee is saved from Gibbs shooting the messenger when FBI Agent Fornell, accompanied by his fellow agent Charles, arrives and admits to being the guilty party.
Victor Gera was actually an undercover FBI agent, who had recently gone missing. The Bureau hoped he was still alive when they saw NCIS access his fingerprints in AFIS. Gera is the latest casualty in Fornell's longtime pursuit of Mafia kingpin Jimmy Napalitano, who has discovered every FBI infiltrator sent into his organization. The FBI suspects a mole, specifically Fornell. No sooner has Fornell explained all this to Gibbs and asked for help, than he is arrested by Agent Charles.
In MTAC, Agent Charles shows Gibbs and Tony live surveillance video of Jimmy Napalitano and his son, Rickey. Ducky identifies the burned victim as Frank Pilato. Agent Charles explains that Pilato disappeared five years ago, before he was to have testified against Jimmy. Pilato was killed long ago, then his body was frozen. Years later, after everyone had stopped looking for him, he was dumped at the bone yard.
Abby finds two types of blood on Agent Gera's face, one of them his and the other not. Perhaps the other is his killer's. Gibbs orders McGee to find a way of obtaining Rickey Napalitano's DNA. McGee learns that Rickey had been hit with two paternity suits, both of which he beat with a DNA test. While the court's records are sealed, the records of the lab which conducted the tests are not.
Fornell is found in his jail cell, hanged with a bed sheet. Agent Charles insists that Fornell didn't take his own life. The warden says he was the only other person in the cell that day, to cut down the body.
To obtain Rickey Napalitano's DNA records, Tony and Kate visit the lab posing as a quarrelsome couple seeking a paternity test. Kate eventually asks if there's another place where she can wait, away from Tony. The receptionist directs her to an empty examination room. Kate then sneaks into the lab's file room and photographs Rickey's records. The second blood type on Agent Gera's face is Rickey's.
Gibbs and Tony arrest Rickey for Agent Gera's murder. Jimmy Napalitano is present, and Gibbs offers a deal. If Jimmy tells him by sunrise who his FBI mole is, Gibbs will let Rickey walk. That night, Jimmy accepts the deal and arranges to meet Gibbs in a local park. Each of them will bring only one person for backup. Gibbs takes Agent Charles, who will know if the person Jimmy brings to exchange for Rickey is an FBI or Justice Department agent.
At the park, Jimmy arrives with one of his own men. But Gibbs is prepared for the double-cross. He asks Jimmy, "Do you know what Primacord is?" and presses the button on a detonator. An explosion blasts a limb off a nearby tree. Gibbs then wraps another length of the explosive around Rickey's neck, and says they can still deal. Jimmy only has to tell him who his FBI mole is. After a moment's hesitation, Jimmy glances at Agent Charles. Gibbs says, "That's what we thought." Jimmy's backup then fatally shoots Charles. With nothing left to bargain with, Jimmy abandons his son.
The next day at the office, McGee wonders how Gibbs knew that Agent Charles was the mole. Tony and Kate tease him about learning to think outside the box, and expecting the unexpected. The three of them get a lesson in the latter when Gibbs enters with an alive and well Agent Fornell. When the FBI realized that Fornell was innocent, they staged his suicide to get him out of jail without tipping off the traitorous Agent Charles.