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.

A boarding party from a Coast Guard cutter visits a foreign-flag cargo ship; no crewmember is visible, but a gunman kills a petty officer. The NCIS and the CGCIS investigate. Gibbs, Borin, and the gang sort it out and serve justice.

An aircraft crashes short of Dover AFB, Delaware, while carrying the remains of six Marines from Afghanistan; Abby does not find the DNA of one of the six; Gibbs and others consider the possibility that the one is still alive. [Continued.]

Gibbs and Ziva fly to Afghanistan to seek 1Lt. Flores or her body; Abby learns where she might be; an extraction team finds and saves her. Back in the USA Gibbs and the gang anticipate what's next, find a bad guy, and prevent an explosion.

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.

While Gibbs and Tony man a protective detail for the SecNav, a gunman shoots the secretary; the NCIS investigates quietly with the help of Dr. Ryan. Blackmail is involved; the gang and Ryan figure it out and find a hacker and the bad guy.

After the attack on NCIS, the President orders all agencies to pursue Harper Dearing with "extreme prejudice". Meanwhile, Ducky tries to recover from his heart attack.

Gibbs and company continue to investigate the killings at Vance's home, seeking whoever hired the shooter; the gang identify the hit man and later figure out who's responsible. Ziva buries her father, and Vance and the team bury Jackie.

Parsons gripes about his project; then a bomb explodes, killing the SecNav; Gibbs volunteers for a spec op, which takes him to Iran, where he runs into Parsons, and where they investigate. Tony tries to pursue Ziva in Israel. [Continued.]

In an effort to find the terrorist Parsa, Gibbs and the NCIS team track down one of his cohorts using evidence from the drone attack. Meanwhile, an emotionally shaken McGee struggles with the ramifications of the incident.

Tis the season to be hacking. In a Christmas letter to his father, McGee describes in detail a case in which he, Gibbs and the rest of the NCIS team investigate the hackers who are responsible for the Internet going down in the D.C. area.