With his help, they track down the real culprit, the corrupt CIA handler who was in charge of the money.
The team investigates the death of a radio DJ and a naval officer who were both killed live on air, and their job becomes more difficult by the discovery of various suspects.
Using an elaborate ploy, the team manages to trick the kidnapper into revealing where he was hiding the girl and arrest him.
Meanwhile, three interns are assigned to NCIS; Abby is suspicious after her last assistant's (Chip Sterling in Season 3) attempt to kill her, Palmer feels ineffective after Ducky bonds with his intern, and Mc Gee must contend with an intern who shows no interest in law enforcement or field work at all.
While searching for the murderer, they inadvertently uncover a large domestic terrorist group composed mostly of wealthy homeowners living in a gated community.
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.
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.
NCIS responds to an emergency phone call after Heather Dempsey, a Marine bomb technician, shoots and kills an intruder in her home.
Dempsey initially evades the investigation, but the team quickly find evidence she was not alone at the time.
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.