EJ and her team take over the P2P case; Gibbs and company investigate the death of a Navy woman officer. The solution, first believed to be simple, proves to be complicated. The killer jumps Ziva, and the gang pounce on him. [Continued.]

EJ and her team investigate yet another P2P murder; the victim is an NCIS agent from Norfolk; Gibbs and company pitch in, as does Franks. Kort, a CIA agent, spills in a briefing. Both Franks and EJ encounter the prime suspect.

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.

Tony, during his task for the SecNav, took fire and sustained a concussion, and he acquired the bloody badge of some other NCIS agent; however, he has no memory of his activities. Gibbs and a shrink help Tony to begin to regain his memory.

Two boys find the body of a Navy commander in a quiet suburban neighborhood; Gibbs and company investigate. EJ Barrett reappears from her hiatus but remains a target. Another man dies, and the gang protect EJ and find and catch the killer.

A fire in a warehouse in Baltimore brings in the NCIS; they find connections to Watcher Fleet. The gang work with a city arson investigator with a mysterious connection to Tony.

Dorneget gets a surprise from a dentist; Gibbs and company continue to investigate Dearing and the thermite incidents. Dearing visits the Navy Yard and messes with Gibbs. Moves and countermoves abound; Vance disappears. [Continued.]

Gibbs and the gang continue to pursue Dearing, the explosions, and the disappearance of the director; Dearing continues to mess with Gibbs and Ryan. After another explosion and another death, disaster strikes at the Navy Yard. [Continued.]