Gibbs's boat, which he gave to Franks, drifts, with two bodies aboard, into the Naval Station at San Diego. Vance and the team investigate. Franks and two relatives show up at Gibbs's house. The gang solve the case and make an arrest.

Gibbs and Tony follow EJ and her team to a nearly vacant building; they find that the P2P murderer has killed Levin, seriously injured Cade, and kidnapped EJ; Gibbs pursues the suspect and EJ; he finds her, left to suffocate. McGeek traces a phone number to CI-Ray (Ziva's boyfriend). Ducky, with help from Gibbs, explains the changes in the MO of the killer. From Levin's left forearm EJ secretly removes a small object. Ziva tries to intercept Ray, but Cobb, the suspect, intercepts and kidnaps her; later, while Gibbs, Tony, McGee, and EJ are present inside a hotel room, Cobb arrives, enters, and surrenders, but he refuses to tell where he put Ziva. However, Abby provides clues to a place, where the gang plus Ray find and rescue Ziva, who gives explanations. Back at the HQ, Cobb escapes with two hostages; Gibbs and others follow; a confrontation ends the career of the P2P killer. The SecNav resigns, and his successor gives Tony a highly sensitive and classified task.

Gibbs and company investigate the death of a woman with an ID card of a sergeant in the US Marine Corps; McGee finds that the real sergeant died in Afghanistan three years ago. Gibbs and McGee go to Kabul, sort things out, and do some good.