Suffering from amnesia and having arrived with blood on his badge, making him the prime suspect in an NCIS colleague's gun-murder, Tony has sassy therapy sessions with Dr. Rachel Cranston in between questioning by Gibbs. Told in flashbacks, Tony starts reconstructing his months of top-secret operation, reporting only to Secretary of the Navy Clayton Jarvis, who hand-picked him. Meanwhile Sean Latham, chief of the internal spy watchers, cleans up the mess with his man Casey Stratton, who poses as FBI agent.
Generaly liked model marine PFC Thomas 'Tommy' Hill, who was expected to lead his Virginia small town's home-coming parade, returns from Iraq to his adoptive family mortally wounded and previously sedated heavily. His hard to recover cellphone and his notebook computer's only movement out of town lead the team to a 'second chance' restaurant for ex-cons and a buried cash treasure. However Tommy wasn't the one with the fatal secret in Ernest McCormick's family. Tony meanwhile feels guilty about a mean high-school prank between him and classmate 'Dirty' John Smith.
Navy lieutenant Paul Booth is mysteriously shot in the Virgina woods just after transferring all his assets to his wife's account. Even she ignored that he actually worked for Vince Westfal's secretive research company, which is a major Defense contractor, founded by the late Max Ellswood. To McGee's shock, Booth was in contact with his own grandmother, rebellious academic Penelope Langston. She and reporter Andrew Pike know about the crucial, top-secretive research project.
The NCIS team searches for the person and motive behind a contract killer targeting a Navy Lieutenant Commander. Meanwhile, Abby uncovers new information about her family after undergoing tests for a kidney donation.
When the Coast Guard boards a cargo vessel at night, a hidden shooter kills one of the officers. No crew is aboard, a Lebanese family of four, all aspiring asylum, is found locked inside. The father, under an alias, is identified as a former anti-US bomb terrorist. Forensics show there was no crew since at least a week. Ziva bonds with the mother, who is reluctant to believe one of her sons may be a killer even when confronted with their family past.
As the NCIS team continues its search for a missing Marine, Gibbs and Ziva travel to her last known whereabouts in Afghanistan. Meanwhile, Tony reveals his deepest fears and Gibbs is forced to relive events from his past.
After Anthony DiNozzo, Sr. is found in a car with a dead body in the trunk and no memory of the previous night, the NCIS team must figure out if he is capable of murder. Meanwhile, Tony is sidelined for this case and must go against orders to try and prove his father's innocence.
Navy Captain Jake Marsden is killed in a hotel room. His pregnant partner Marine Lieutenant Emma Reynolds, an Afghanistan veteran herself, needs NCIS's protection after seemingly mysterious attempts on her life by Rusian mobsters, but mistrusts the team too. This arouses gripping memories of his late daughter, rendering Gibbs personally committed. The team works out the key is in Afghan real estate and the child's father. Ducky meanwhile coaches Palmer to grow a spine when his impossible to please, insufferable father-in-law-to-be Ed Slater visits NCIS.
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 Dan Garscott 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. Garscott 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, ...
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 ...