The season story arc involves Ziva's largely-unseen boyfriend, Ray, and the CIA continuing to meddle in NCIS's day-to-day workings.Notable events include the terrorism and internal affairs threat during the "Enemies" two-parter, and the arrival of another Major Case Response Team from Rota, Spain, the team that Tony was offered to be lead of in the beginning of season four.NCIS responds to an emergency phone call after Heather Dempsey, a Marine bomb technician, shoots and kills an intruder in her home.
The team is involved in an international incident as they investigate the murder of an American petty officer whose case is connected with a Royal Navy ship.
Complications ensue when someone tries to get the ship to depart before NCIS can properly investigate.
Paloma Reynosa, head of the cartel, plays a game of cat and mouse with NCIS as she makes a wide trail through the US, expanding her cartel's influence.
Tensions erupt when Alejandro Rivera (guest star Marco Sanchez), calls Abby on her bluff to send the report on the Pedro Hernandez murder and threatens her in front of Gibbs.
They discover that the murder was over a large amount of stolen CIA money, used to pay off warlords and dictators in Afghanistan.
At first, the team suspects that the Royal Navy liaison officer is responsible, but quickly find out that he is actually an MI6 agent who was framed for the theft.
The season ends on a five-part story arc involving the Port-to-Port killer that menaced both teams. Following Jackson Gibbs' (guest star Ralph Waite) confrontation with Paloma Reynosa (guest star Jacqueline Obradors), he is placed in NCIS protective custody at his son's house.
A few months later, the death of a helicopter pilot embroils the team in the Reynosa Cartel's vendetta with Gibbs, making each team member a target.
Dempsey started a relationship with the agent to learn Abbott's new identity and location.
When he learned that Dempsey was searching for him, Abbott hired the hitman to kill her before she could kill him.
With his help, they track down the real culprit, the corrupt CIA handler who was in charge of the money.