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 Marine private first-class returns from Afghanistan to his hometown in time for a welcoming party for him during homecoming week; however, when he arrives, he staggers in, mortally wounded, then collapses and dies; Gibbs and company investigate; Ducky says that death resulted from stab wounds. Ziva spots a piece of evidence, but it becomes hard to obtain it; Tony and Ziva find that the victim had started with a disadvantaged childhood, became adopted into a military family, then enlisted in the Marine Corps and established an impeccable record. Abby finds some interesting electronic evidence, then Tony and McGee find something while hiking, and McGee makes some new friends. Abby makes important discoveries; the gang learn about multiple identities, a forged letter, stolen funds, and a hidden relationship, and they rescue from death a man who then dies. Eventually they put the pieces together, and they get help for someone who needs help.

A Naval Reserve lieutenant dies of a gunshot in Washington, DC; Gibbs and company investigate; the victim has one of McGee's cards; McGee learns that his paternal grandmother is involved. The gang assemble the pieces and catch the bad guy.

In Washington, DC, near the Capitol a van accidentally hits and critically injures a pedestrian, who proves to be The Cooler, a wanted contract assassin, whose next target appears to be a Navy lieutenant commander; Gibbs and company investigate the target, LCdr. Geoffrey Brett, and his circumstances, including the threat. The Cooler briefly regains consciousness in a hospital, then dies before an NCIS agent reaches him. Ziva acts as Brett's protective escort, but he ditches her. Tony and McGee meet a CPA, then she dies. The three musketeers gather pieces of evidence and, with Gibbs, put them together; Brett says that he needs a lawyer. Meanwhile Abby volunteers to become an organ donor, learns more about herself, visits a pet-rescue center, meets someone whom she admires, examines her own feelings, and has a serious chat with Gibbs.

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.

At 04:19 in northern Virginia an 18-wheel truck accidentally and fatally hits a Naval Reserve lieutenant who had swerved and woven on a freeway, parked on the left side, and walked toward an emergency call box on the right side; Gibbs and company investigate. Ducky sees telling evidence at the site, finds an explanation in his workshop, and offers a theory. The gang check out the obvious leads; Ducky meets and courts an attractive and interesting new ladyfriend. While hiking through a state park, the team find a dead SUV and a dead body under circumstances similar to those of the other victim; this vic is a civilian, but his estranged wife is a Marine on active duty in Afghanistan. When Duckman again sees his new honey, he gets two real surprises. Meanwhile, Gibbs and the gang figure out what's happened, so they head out to help; they wrap up some loose ends; Gibbs offers Duck a ride home.

Diane, the mutual ex-wife of Gibbs and Fornell, gets help from them; Victor, her current husband, has disappeared; they and the gang find the pieces, put them together, find the bad guys, and deal with them. Diane gives Gibbs a watch.

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.

DiNozzo Senior is found unconscious, in a car with a murdered naval officer in the trunk.

A Navy captain dies by gunfire; Gibbs and company investigate; the gang meet Emma, a pregnant Marine first lieutenant, who says that she's the real target. The team figure out the pieces, and they deal with the problems and the bad guys.

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 Navy woman lieutenant commander dies of gunfire; she has served as a Naval attaché overseas, and her husband is a detective for the Metro PD; Gibbs and company investigate; the widower's help does not help, but the gang solve the puzzle.

At a diner an unknown person with a drawn pistol approaches Gibbs, who deals with him; then Gibbs experiences flashbacks and fantasies, which Franks explains. The next day McGee announces a decision, then the gang gear up and head out.

A civilian and a Navy captain die of gunfire in Washington, DC; Gibbs and company investigate; the Duck sees unusual undergarments, which are also costumes. The gang solve the puzzle and nab the bad guys; Wendy reveals something to Tony.

When two burglars enter a home in Arlington, Virginia, in the burbs of Washington, DC, they find the hanged body of a man; the victim proves to be that of a psychologist (with a PhD degree), who was also a Naval Reservist on active duty, and who held a high-level security clearance for his work, which included consulting with the US Department of Defense (DoD) on a psy-ops program; while Gibbs and company investigate, they soon encounter Dr. Rachel Cranston, who was a colleague of the victim, and with whom they've dealt before. Another mind-gamer shows up, and Abby finds a mind game. McGee plays with some electronic toys, and the other members of the gang pursuit other leads; Gibbs orders the team to concentrate on paper, and he kills a bug. Despite much interference and misinformation, the gang solve the puzzle and bust the people responsible. A payroll clerk discovers a number of mistakes, and Gibbs receives an interesting phone call at 04:00.

When Gibbs meets with a Navy chief petty officer and his attorney (to make a deal), the CPO collapses and dies; while the gang investigate, they find a connection to an illicit arms dealer. The team figure it out, and everything works out.

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.

While on liberty in Baltimore, Maryland, a boatswain's mate second-class dies of a stab wound; Gibbs and company investigate; the prime suspect is a brother-in-law of Vance. The team persist, Abby solves the case, and they nab the bad guy.

A picnicking couple encounter a dead body, which proves to be that of a first lieutenant in the US Marine Corps; after Gibbs chats with Dr. Ryan, he and the team investigate; the gang see that the victim had plummeted from somewhere in the sky after he had first been beaten, stabbed, and shot; in one of his pockets they find a challenge coin, which they trace to a woman commander in the Navy Chaplain Corps, who is on duty with a relief team in Colombia. Ducky finds curious clues, and Abby interprets them (connecting to Colombia); Ziva communicates with Monique, a contact in Colombia, who repeats a rumor about the disappearance of the Marine and the chaplain; Ryan gives Gibbs a tip. Tony, Ziva, and a second woman chaplain join Monique in Colombia; someone else provides fireworks; then Gibbs interviews a mule. McGee continues to dig, then Ziva and Monique meet a couple and get answers. Tony, Ziva, and two chaplains fly back home with their new friends.

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.

Gibbs and company continue to investigate an explosion and a fire; Tony, McGee, and Ziva work aboard aircraft carriers; Ducky and Abby provide much support. Tony and Ziva nab a bad guy, who tells who hired him and why. [Continued.]

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.]