Aboard Air Force One a Naval officer dies after eating with the Potus, then a Marine officer (connected with AF1) also dies in Georgetown in the same way. Abby identifies the cause, and Gibbs thwarts an attempt to assassinate the PotUS.

During a training jump a Marine dies when his main chute fails to open, and he fails to pull his reserve chute. Kate joins the NCIS team, and they investigate; they identify not only the murderer and his method but also a drug connection.

US Navy commander "Seadog" washes up dead on a North Virginia beach. 2 dead, alleged drug dealers are found nearby. All 3 are shot. NCIS, joined by DEA and FBI, investigate.

A chef finds a naked sailor inside a freezer at a restaurant in Rota, Spain, during a port visit by USS Enterprise; shortly afterward at sea another sailor freaks out on the flight deck; soon one of them dies. Gibbs and his team solve it.

Workers find the decomposing body of a man, apparently a submariner, inside a drum of acid. The team treats the case as both a murder and a theft of identity. Gibbs and Kate go aboard a sub at sea, find the bad guy, and save the crew.

A naturalized petty officer of Egyptian descent dies in the US from massive bleeding due to an intestinal blockage caused by emeralds; he had just arrived from Camp Delta at Gitmo. Gibbs and others investigate at Gitmo and prevent a murder.

Two Marine majors supposedly die during a classified operation in an undisclosed foreign country; one of them purports to call home. The team investigate; they encounter much interference, but they succeed, and they reach a happy ending.

A young lady emerges from a shallow makeshift grave in Rock Creek Park, Washington, DC; although amnesic she says that there's no time, that there's a bomb aboard a Naval vessel, and that people will die. A passing driver aids her and calls 911; the Metro PD responds, then calls the NCIS. Gibbs and his team investigate. Kate befriends the victim and takes her into her pad, and she slowly recovers a few memories. Gibbs finds a key, then Abby figures it out, then Gibbs and Tony find a body. The ship in question proves to be ashore and inside a building. The team learn the name of the victim, then she begins to recover more memories than she reveals. Eventually she confronts the person responsible for her treatment, and she drops a surprise on him.

A Naval officer, a SEAL diver, dies of a stab wound after swimming while testing a classified handheld sonar device, which disappears. An anonymous caller reports the murder. Gibbs and the gang find both the killer and the missing device.

A Marine recruiter dies in his office from a single shot; Gibbs and the gang investigate; then a second one dies likewise. The Gibbs group expect another murder, so they set a trap, and it works; Tony and FBI agents capture the sniper.

A Navy dentist from a Naval air station dies of a single shot to his back, apparently in an execution-style murder; the NCIS investigates. Two more men from the same Naval air station soon die identically. Gibbs and company figure it out.

A Marine colonel disappears during an ambush in Iraq, as does $2M in cash; he re-enters the US under an assumed name; the FBI seeks him, and so does Gibbs, with whom he served while on active duty. Gibbs finds him and figures it out.

A foreign agent enters the autopsy room via an unconventional method; he then takes captive Ducky, Gerald, and, later, Kate. He demands evidence pertaining to a body in the room. He eventually asks to see Gibbs, who obliges him; he loses.

The gang mourn the death of Kate; they recall her and deal with her death. 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. [Continued.]

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.