Streets kids discover the corpse of a navy commander whose car crashed. He had been shot fatally, while driving, from pro-sniper distance. Thus the team finds missing, almost presumed-dead NCIS special agent Erica Jane 'EJ' Barrett. Tony must guard her in a safe-house, both being probable targets of the elusive but extremely deadly Phantom unit, whose member Casey Stratton is recognized on a neighborhood security recording. Their boss, Sean Latham, maintains Stratton's innocence to the navy secretary and meets to pass on the safe-house.
Navy lieutenant commander Maya Burris, naval attaché in Cairo on holiday, is found murdered in a building under construction, probably by an expert. Her distraught husband, metro detective Nick Burris, won't idly wait, mistrusting federal agents. The team concentrates on her frequent trips to Islamabad, meeting a Jihaist extremist. Ziva is bitter, being stood up by CIA fiancé Ray Cruz, worse when the reason becomes clear.
Retired Navy Captain Jack Wallace was shot with Dexter Murphy in the last's shop. Both belonged to a costumed 'superheros' neighborhood watch society. Tony is assigned as 'press liaison' with his last significant ex, reporter Wendy Miller, who got an exclusivity exchange deal from the director.
Navy Reservist Dr. Robert Banks died from a bizarre cardiac arrest, as forensics gradually uncover provoked in various devious ways. He devoted his life to his spoiled daughter and his job as gifted researcher in the US navy's PsyOps agency. The team finds on its way his MD, Dr. Rachel Cranston, as well as people from PsyOps, who play their expert deception games, forcing Gibbs to resort to old-fashioned methods.
Navy Chief Petty Officer Leland Wiley's attorney makes a deal to get him out of a minor prosecution in exchange for information against the elusive arms dealer Agah Bayar. Tailing him and his lady friends (actually not just that) proves problematic as other agencies claim priority and invoke top-secret. McGee doesn't enjoy coaching present Probie Ned Dorneget's first field assignment, but even his worst error works out in the end.
Gibbs and Tony are on security detail when the Navy secretary Clayton Jarvis attends a seminar with family friend Philip Wickes, whose steel company expects to loose its crucial US Navy contracts due to a 'green program' to switch to polyester ships. Jarvis is hospitalizes in lethal danger after a shooting, but it's staged. Gibbs' team is to investigate discretely, jointly with Psy Ops. Wickes's suggested suspect is found murdered at home and involved in an implicit blackmail. McGee takes on a masterly hacker, which leads to yet another motive.
Popular Navy Petty Officer Third Class Caleb Adams is found fatally stabbed in the port. His blood is on the hands of mechanic Michael Thomas, Vance's brother in-law and regularly messing up protégé, who claims to have found Dan and just sought help. Adams was badly bruised hours before his stabbing. The only other man who failed to report to his ship after shore leave is his youth buddy, Brian Smith. Vance tries to shield Michael, whom he even takes home, and have Brian charged. Gibbs and Tony however find out the whole sad truth, involving hopeless love, gambling ...
Lieutenant Larabee's corpse is found, thrown from a Navy airplane. A rare fungus enables tracing the flight to a Colombian drug cartel's home region. Psy Ops's Samantha Ryan indirectly tips off Gibbs the top-secret flight was CIA-sponsored, the ex-con pilot has an airtight alibi. DiNozzo is in charge of a mission to Colombia, where Ziva calls on close friend Monique Lisson, now working for a local missionary organization, and a chaplain who insists to come along looking for her missing colleague, who was also aboard. Jimmy Palmer is choosing a best man.
A critical product tester in an innovative Baltimore electrical equipment company, which turns out to have a top-secret navy contract relating to the Phantom fleet, dies by arson in the warehouse where he filed 'non-crucial' papers. The unnecessary but masterly use of thermite explosive inspires consulting life-jailed expert pyromaniac Billy Wayne on arsonist logic. Tony is most uncomfortable collaborating with the Baltimore PD fire investigator, his younger youth acquaintance Jason King, who bears a viciously unfair grudge. They barely survive a thermite trap aboard ...
Investigating the late thermite arson suspect Johnson's home put the team on the trace of Tobey Abbott, representative and technician for a Navy-contracted electric installing firm with a grudge after failing muster. Cracking a Korean alphabet code suggests the next target. It's in Naples, so Tony and mates join local security chief NCIS special agent Stan Burley and apprehend the henchman who knocks Stan down, albeit he knows very little.
The team now knows Harper Dearing masterminded the sabotage bombings and realizes his motive is his son's fatal accident in naval service. Catching him physically proves very hard, despite daring provocations. His firm's manager Vincent Maple's own machinations are found out. Meanwhile more secret fleet-type tracking devises are found and Jimmy palmer fears 'best man' Abby's top-secret bachelor night plans.
The team is now certain that Harper Dearing instigated the explosions but finds him elusive. He manages to kidnap director Vance and lock him in a tomb with a Junior officer who died in the same avoidable accident as Dearing's late son. It turns out he was also involved in bullying junior, the root motive for Dearing's latest terror acts, the latest of which is against a retired NCCIS officer. Psy Ops Samantha Ryan's adolescent son Parker is shown a potential target but spared. Gibbs makes a vague deal with life-jailed secret fleet hit-man Jonathan Cole, presumably ...
After Harper Dearing blows up Vance's car and destroys most of the NCIS building, the agents increase their efforts to find him. The president gives permission to kill him if necessary. Ducky is in a hospital after his heart attack.
Another NCIS employee is found a few weeks after the explosion at the NCIS building, but this agent was murdered. While investigating the crime, the team also has to talk to a crisis counselor to deal with the after affects of the explosion.
Ducky exhumes the body of a man who died 12 years previous. Abby finds proof the man was actually murdered. When the team investigates a current death, they find a connection to the murder 12 years ago and Gibbs assigned Ducky as lead agent.
Crew members from a downed helicopter washes ashore. The missing pilot is later found in the water, dead from a gunshot wound. The NCIS team finds there was a conspiracy plot with the other crew members. The pilot was not part of the plan.
A man is killed in a borrowed sports car belonging to a wealthy business man. The murder weapon leads the team to a pawn shop where Gibbs finds a Medal of Honor belonging to his namesake, a man who used to be his father's best friend.
Two men who recently returned from the Middle East are attacked. One dies. The other suffers from post-traumatic stress and has a hard time separating what happened in the Middle East and the current attack. Gibbs helps him figure it out.
Gibbs continues to help Sgt. Wescott retrace his steps in order to determine what happened. Abby plans a holiday meal for the team. Ziva tries to get tickets to an opera performance but cannot. Tony finds a way to help Ziva.
A young girl's father is murdered during a kidnapping attempt, while her best friend is taken. The team tries to track down the kidnappers while trying to figure out why she was taken. Meanwhile, an old friend of Ziva is coming to visit.
Agent Fornell is targeted by a hit-man. Since it was a Navy man, Gibbs team steps in for the investigation. Fornell & Gibb's ex-wife is undercover and working on the case that caused the hit to Fornell.
A Navy officer's husband is murdered. The team investigates and find the man connected to $100 bills, that were to be destroyed, stolen from the Treasury Department. Tony's dad visits and tries to create a family holiday for him and Tony.