Two years after a Naval officer and his car disappear without a trace, a PI, seeking a reward, finds on the bottom of a lake the car and the skeletal remains of the missing man. After false starts Gibbs and the team solve the mystery.
Ducky faces the "meat puzzle" of concurrently reconstructing three cadavers dissected into many small pieces. Ducky IDs one body, and the gang ID the others and a fourth. Ducky is the fifth target, but the team find him and save him.
A woman reports the strangulation of a sailor in his dress blues; the Metro PD responds to a 911 call, finds no body, calls the NCIS, and turns over the case. McGee, Gibbs, and the others seek evidence, and they find it and a solution.
A Marine sergeant dies while hiking with his wife and his best friend, another sergeant; the gang investigate. Ducky finds a wood-fiber fragment, and Abby reconstructs video footage; Gibbs questions, and the team put it all together.
The body of a woman sailor appears in bed in Norfolk with a bartender, who swears that he went to bed with a different chick. NCIS investigates. Death occurred by a huge OD of meth. Another woman dies. The gang find answers and killers.
A neighbor of a petty officer opens a package from Paraguay containing two human eyeballs mistakenly delivered to the mailbox of the neighbor. Gibbs and company investigate. Kate and Tony make discoveries in Paraguay, then they return.
A petty officer enters a bikini contest but fails to appear on stage when introduced; later someone finds her body face-down in a toilet bowl in a women's restroom. Tony enjoys his work; the gang pursue the leads and find the killer.
A petty officer reports that someone has assaulted her; the NCIS investigates. The victim has a mental illness and has had an affair with a captain under investigation by the FBI; she soon dies by murder. The team figure out everything.
An NROTC midshipman stumbles over the body of another middy at 02:00 on the campus of their university; a third mid has disappeared, and McGee finds his body. Abby helps. Gibbs finds the killer, then Kate and Tony cuff him.
A hospital corpsman stows his gear in a self-store room; after 10 months he dies in action in Iraq; then the skeletal remains of a high-school friend turn up in his storeroom. Despite local resistance Gibbs and company solve the mystery.
Tony opens a letter, literally SWAK, dispersing a fine white powder; the gang does the drill. Kate and Tony get a free trip to Bethesda. Gibbs and company find both the bad lady and the solution of a two-year-old rape case at the USNA.
Tony returns early, in time to rejoin the team in an investigation of a shooting of two Naval aviators. Tony finds a bomb, then it explodes; Gibbs says that someone has again tried to kill the NCIS gang, which loses one of their members.
The gang mourn the death of Kate; they recall her and deal with her death. Meanwhile Ari puts a round into Abby's lab, and the NCIS gets a new director, who shares a history with Gibbs. Ducky accepts an invitation to an unusual meeting.
Ducky meets Ari, Tony follows Ziva, Ari secretly betrays Israel and Mossad, Ziva passes cash and a fake passport to Ari, Gibbs and Jen seek Ari but miss him, Ari finds Gibbs, and Ziva finds them. The gang attend Kate's funeral in Indiana.
Gibbs again questions a condemned serial killer whom he arrested 10 years before. The killer, three days from execution, has offered to reveal the locations of the bodies if he gets to talk with Gibbs. The gang solve that and much more.
Ziva returns. A 140-year-old iron casket shows up at the Smithsonian Institution; it contains the body of a Marine staff sergeant on a UA, so Gibbs and company investigate. The team chase the clues, follow a map, and figure out the story.
A sailor dies of a gunshot and the resulting car wreck. Gibbs and company investigate; the victim first appears to be an impostor, but Abby shows otherwise. The impostor is another man. The gang figure out the death but not everything.
Two wives of two deployed enlisted Marines disappear; the NCIS investigates. McGee recalls something, and that gives the team a start. The two wives went into business together online, but it goes out of control. The gang figure it out.
A six-year-old boy sees who kidnaps his father, a Naval officer who works with a highly classified online-encryption system; the boy calls the NCIS, so Gibbs and the team investigate and eventually solve the crimes and recover the father.
Tony and Ziva go undercover and under the covers as assassins, a married couple, who recently died, but who apparently have a contract to execute at the Marine Corps birthday ball in Washington. The NCIS gang figure it out and work it out.
The amputated legs of a young woman turn up aboard the Marine Corps Base, Quantico, Virginia; Gibbs and company investigate. Forensic evidence implicates Tony because a pro has framed him. Abby works hard, and the gang find the bad guy.
Three supermodels take part in a reality show aboard the Marine Corps Base at Quantico; one of them disappears but shows up dead on a fence; the NCIS investigates. The victim's boyfriend shows up dead at a motel. The gang figure out all.