The episode opens with Gibbs on a beach in Mexico discovering the body of male, face down in the sand. Then a man puts a gun to Gibbs' head.
Flash back to four days earlier.
Our team investigates the murder of Special Agent Lara Macy, whose charred remains are found in a BBQ pit in Annapolis - NCIS jurisdiction.
Before her murder, Macy was investigating a rape case of Pettty Officer Kaylen Burrows which may suggest that the rapist may also be the killer.
Evidence leads to Tyler Hammond, a privileged college student, who was in the same bar in France as Burrows at the time of the attack.
It gets more twisted when they learn that Burrows was not only assaulted by Tyler but also by Tyler father Randall Hammond, DC construction tycoon.
But they didn't kill anyone.
Ducky discovers that the blade used to slice Macy’s throat was from an army knife and the precision at which she was cut was brutal and professional.
Gibbs then realizes what he'd already suspected - Macy’s killer had nothing to do with the rape she was investigating but everything to do with Gibbs.
A man claiming to be NCIS had showed up to "investigate" at Macy's mom's house before Tony and McGee, even, taking some of Macy's notes with him.
Gibbs unsuccessfully attempts to track down Mike Franks in Mexico and leaves a message for him to use Rule 44.
Vance forces M. Allison Hart to come clean as to Colonel Bell’s motives and discovers that Bell has been gathering information on Gibbs for months.
Macy’s killer turns out to be dishonorably discharged Lt. Dean, Col. Bell’s right hand man. That's who points a gun at Gibbs at the end ... but it was not Franks' body Gibbs was standing over, but that of Col. Bell.
Meanwhile, Vance approves the return of Pedro Hernandez’ body to Mexico as Abby has wrapped up the cold case she’s been working on. However, she is torn as to what to do with the file because of Gibbs' link to Hernandez.