Sam stopped and arrested for murder. Hetty's there at his arrest and says he needs to comply. His case is being handled by the Department of Justice. While the case is pending. Callen taken out of the field and put on desk duty.
Hetty puts the Ops center on stealth duty. They are going to investigate Sam's case. Leyla Walden was killed in Van Nuys and Sam is being charged. He was undercover at the time of her death.
Deeks and Kensi investigate the murder scene. Meanwhile, Callen hides in the backseat of the FBI agents' vehicle in order to find out they have on Sam. The agent reveals they found Sam's DNA on the victim. Back at NCIS, they review the footage of the time of the crime and someone looking like Sam entered and left the premises. They also compare the DNA found on the victim and it matches the DNA sample Sam provided them.
Deeks and Kensi visit the deli Leyla frequented. While there Nell sends them a photo of a man who was seen on surveilliance video from the area. The deli employee identifies him as Ray Turner. He's made it his mission to uncover fake SEALs. Given Sam's covers, they wonder if Turner targeted Sam.
Deeks finds an arsenal of weapons at Ray Turner's place. When he enters the room, Turner comes after him and threatens to shoot him. Deeks keeps his back to Turner to prevent him from shooting in self-defense and allow Kensi enough time to get into place. They arrest Turner.
Turner denies knowing Leyla. He continues to deny it even after Deeks shows him the photo of them together. Kensi tells him Leyla's dead. He doesn't seem to know.
The two FBI agents are having sex in a hotel when Callen shows up. He breaks into the room and they run out partially clothed. Granger takes a photo of them in a compromising position and threatens to out their relationship to their spouses and bosses.
Granger gets Sam out of lock up. First thing Sam does is go in to see Turner to talk SEAL-to-SEAL. Turner wants to check out Sam with some of his contacts. They let Turner loose and follow him. Turner goes to a boat "Easy Day," and then swims around and video calls Sam. As they are talking the boat blows up.
Turner was looking into Jeremy North, a former SEAL, who had a defense training school and planned going into private security. Leyla was his bookkeeper. North killed Leyla because she was going to out him as a fake Navy SEAL.
Jeremy North looks like Sam. He was in the Navy at the same time as Sam. They hadn't seen each other in years. North, a.k.a Stevens, had a dishonorable discharge.
Deeks and Kensi show up at North's self defense school as students to look for him.
At the same time, Sam, Callen and Turner go to the office to investigate. They find a guy shredding documents. He pulls a gun on them and they shoot him. They find an identity theft factory. When going through the fake identities, they find an ID that Sam lost years prior. When he stole Sam's hat, they hit gold since Stevens looked like Sam.
Stevens' club employee, Heidi, recognized Deeks from his time in the LAPD. He once helped her when she was a working girl. She agrees to help them catch Stevens. She's supposed to make a drop for him. She shows up and has a laser pointed at him. Sam covers thew woman from the shot while they go after the bag.
Sam goes after the shooter. It's Stevens. They end up face-to-face. Sam drops his weapons and takes off his vest. He wants to fight Stevens, "no guns, no badge, just me and you." Sam gets him right away and backs off giving him another chance. Sam makes a fool out of Stevens. Sam gives Stevens a hatchet to use against him. With a deadly weapon, Sam says he can beat him to death.
Sam knocks him down and belittles him. Stevens cries and gets arrested.