Army officer Richard Booth is newly retired from his Delta Force unit, where he worked to eliminate targets in the War on Terror. As a civilian, he was planning on heading back to Afghanistan in order to collect a bounty on a high-profile bomb maker he was investigating. However, Booth is found tortured and killed and NCIS is called in to solve his murder.
Delving into Booth's personal life, it's discovered that his son, Brandon, has been estranged from Booth for years. He's a possible suspect, but when Callen and Sam question Brandon, he's suddenly attacked. The team manages to shoot the attackers but Brandon escapes.
Meanwhile, the team questions Jafar Khan, who worked with Booth in Afghanistan as an informant. He claims that he and Booth were partners and they were going to go after the huge bounty together. There is evidence that Jafar hired men to kill Booth so that Jafar would be alone to collect the bounty. Due to diplomatic immunity in the US, however, Jafar can't be brought in for further interrogation.
Deeks tracks Brandon down, and he seems to have a rapport with the younger man, since they both have distant fathers. The connection pays off, as Brandon gives Deeks access to the pictures Booth sent his son. Information on one of the photos indicates that the intel Booth got from Jafar was valid. The team heads to Afghanistan, where they find Jafar using the information he'd gotten from Booth by torturing him. Since they are no longer in the US, Jafar doesn't have diplomatic immunity and he's taken into custody.