Tony is shot and unable to remember what it was all about. He must work together with Gibbs and Dr. Cranston to identify the attacker. Ziva is promoted to Special Agent.
A Marine named Thomas Hill collapses at his homecoming party, having been drugged and stabbed before arriving. As the NCIS team start digging through his past, they discover Hill's adopted younger sister is a twenty-seven-year-old serial con-artist who runs away from her foster families shortly before her "eighteenth" birthday and has a dark secret behind her scam. Meanwhile, Tony begins to feel remorse for schoolyard bullying during his time at boarding school and enlists McGee's help in making amends. However, by the end of the episode, it is revealed that Tony was the victim of bullying and not the perpetrator.
NCIS is assigned the case of Paul Booth, a Navy lieutenant who is shot dead in a park after talking to his pregnant wife. During the process, McGee's business card from his days in Norfolk is found in the victim's pocket, leaving McGee confused as he has no knowledge of ever meeting the victim. Booth was a friend of McGee's maternal grandmother, Penelope Langston, who developed a research project for the military known as the ANAX Principle before the outbreak of the Vietnam War. The ANAX Principle was then shut down for four decades before being restarted. It uses specially bred caterpillars as the basis of a genetically engineered/Biomechanical plague. Booth's killer is revealed as Max Ellswood, one of the original researchers of the ANAX Principle, who killed the lieutenant when Booth planned to reveal the program to the press. At the end of the episode, McGee and his grandmother speak of how Gibbs reminds them of McGee's father. McGee ultimately decides to call his dad whom he hasn't spoken to in seven years. Meanwhile, Jimmy Palmer struggles with plans for his upcoming wedding.
Abigail Borin returns to NCIS when a U.S. Coast Guard Petty Officer, Cooper, is shot while inspecting an incoming vessel. The NCIS team discover that a Lebanese family seeking asylum has stowed away on the boat. As Ziva begins to bond with the family, evidence emerges that Cooper was shot with ammunition sold to the Lebanese government, and Gibbs begins to suspect a political connection. Meanwhile, concerned that he is lonely, the team tries to find the perfect girlfriend for Gibbs, but once they decide on a candidate, Gibbs revealed that he had already dated her, but broke up because "perfect is boring".
An NCIS case changes from accidental death to murder when evidence reveals that a Navy lieutenant died of forced over-hydration. The team discovered that the victim, Jason Simms, had been drugged with ecstasy, causing severe dehydration; this led him to over-hydrate, causing water toxification. When a second victim, Alcott, is found bound to a tree and also dead by way of water toxification, NCIS realize that both Simms and Alcott had failed marriages, and had been members of outreach programs and targeted by a serial killer. Meanwhile, Gibbs meets Ducky's new love interest, Mary (Cheryl Ladd), a woman he met online. McGee realizes that Mary is connected to the same program as Jason and Alcott, and is responsible for their deaths. Mary explains to Ducky that she chose this method of murder because he had said he had "seen it all" in his job and she thought he would appreciate an interesting and novel case. Ducky is disturbed by his misplaced judgement of her, feeling guilty that he did not see her deception sooner.
Gibbs and Fornell are approached by their mutual ex-wife, Diane, when her current husband disappears under suspicious circumstances. The case causes a stir within the NCIS team and they all attempt to find out about Gibbs' past life, much to his irritation.
A C-130 carrying the bodies of Marines killed in Afghanistan crashes, stretching the team to the maximum as they are given twenty-four hours to identify the bodies before they are released to their families. Complications arise, however, when one of the bodies cannot be identified, and 1st Lt Gabriella Flores, a Marine who was supposedly killed in an attack on a local school-building project, remains unaccounted for. Accessing satellite footage of the bombing, the team realize that Flores is still alive, having tried to save two young girls – but moments later was captured by insurgents. McGee and Abby deduce that some of the teachers in Flores' school-building project are actually female insurgents and Taliban-sympathizers sent undercover by a small but highly organized terrorist cell to infiltrate the school. The episode ends with NCIS preparing a rescue mission to save Flores. The case affects the team on a more personal level, especially Gibbs, who reminisces about his time in the Marine Corps, while Tony reflects on the shortness of life.
Gibbs and Ziva travel to Afghanistan in search of Gabriella Flores. After talking with the two girls that she rescued from the school attack, Flores is successfully rescued, but her commanding officer is killed in the process. Back in Washington, Tony discovers that the woman who held Flores hostage has a brother, a university student based locally, and both are members of the same terrorist group. The team continue interrogating the siblings but to no avail. Gibbs, with some help from Vance, takes matters into his own hands as the team races against time to find out the terrorists' next move. DiNozzo attempts to conquer one of his phobias while Gibbs relives a painful memory from his days as a young recruit.
Tony's father awakes to find a dead body in car trunk and has no memory of the previous night. Tony is sidelined during the investigation, much to his annoyance. After clearing DiNozzo Sr., the team must find out who drugged him and why. The episode ends with both DiNozzos spending Thanksgiving at Gibbs' house.
When a Navy captain is killed in a hotel room, NCIS must track down and protect his very pregnant companion from unknown assailants. The team has to contend with terrible weather conditions and having to work on Christmas Eve while back at headquarters, Jimmy is frustrated by his difficult future father-in-law.
The investigation of a Navy Commander's murder leads the team to E.J. Barrett to reopen their investigation into the fake FBI Agent Stratton, who attempted to kill the former and DiNozzo months prior.
During a routine stop in a diner for his morning coffee, Gibbs finds himself shot. He then suddenly finds himself inside a spectral version of the diner where he sees various characters from the past and present, both living and dead.
Dr. Robert Banks, a prominent Navy psychologist, is found dead from an apparent suicide. Gibbs and his team look into the world of psychological warfare when Dr. Samantha Ryan, the head of PsyOps, refuses to answer questions or release information to aid the case.
When a shooting occurs at a seminar on Gibbs' and Tony's watch, Gibbs must work together with both Secretary of the Navy (Matt Craven) and Dr. Samantha Ryan (Jamie Lee Curtis) to find out who leaked top secret information and McGee must pit his wits against an elusive and cunning hacker.
After the corpse of a Marine lieutenant falls out of the sky, Tony helps Ziva and her mentor, Monique, look for a missing Navy Chaplain in Colombia. Jimmy Palmer chooses his best man for the wedding.
NCIS is called in when the Baltimore Fire Department discovers a stack of classified Navy documents next to a skeleton after putting out a warehouse fire. Tony, a former Baltimore PD detective, returns to his former stomping ground and unexpectedly reunites with someone from his past.
In the aftermath of the arson attack aboard the USS Brewer, the NCIS team discovers evidence of it being caused by the same arson explosive from earlier.
