The body of a Marine corporal, minus his feet, shows up in the trunk of a junked car; Gibbs and company investigate. Abby and McGee go to Mexico on business; Abby returns with concerns. The gang figure out who killed the Marine and others.

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.

A family owned mortuary ordered a bunch of caskets from an overseas company. When they go to unload the shipment, they find that one of the caskets already has a dead body. There are ties to a prison break of someone NCIS helped put away.