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.Nicholas Mason, the missing girl's grandfather (William Devane), complicates matters when he arranges a ransom drop without informing NCIS.While the team are working to find out the identity of the kidnapper and motive, Gibbs is worried Mason will take the law into his own hands and potentially cause more damage.Meanwhile, Leon Vance, whilst putting the report implicating Gibbs in a place no one will find it, receives a mysterious text message from Eli David, Director of Mossad claiming "I found him".A teenage girl is kidnapped from her middle school on the Quantico marine base, prompting NCIS to investigate.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 NCIS team raids the community and arrests all of the members, only to find out that they have something much more sinister planned.
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.
Her lover is revealed to be a senior FBI agent; the intruder a hit man.
They learn that Dempsey's brother was shot and paralyzed by a man named Abbott in a gang war, and that the FBI lover recommended protective custody for him after he testified to escape jail time.
With his help, they track down the real culprit, the corrupt CIA handler who was in charge of the money.