Ziva accidently witnesses a political assassination. She learns the FBI wants her so she flees, leaving the NCIS team, lead by Tony, to prove her innocence. The team tries to work without Gibbs since he has retired, but when things get complicated Ziva asks him for help.
Gibbs and the NCIS team look into the old robbery case of a convict who has threatened Fornell and his daughter. Their investigation leads them to a retired sailor who contacted the convict after being sent to prison.
An abandoned car is found full of blood, registered to a missing Navy lieutenant. The NCIS team learns that the missing lieutenant was profiling men, trying to find a perfect man for herself. When they find out that the woman intended to go to a seminar at a local hotel, Ziva goes undercover to find more information. Ducky is busy going through the profiles of the men. Jenny makes a secret offer to Tony.
A Petty Officer is found dead in his car with "NCIS" written in blood on the seat. The investigation becomes complicated when Homeland Security claims that the Russian Spy suspected of killing the officer is working for them.
A Corporal is found dead in a vacant house. The investigation leads the team to his two finances.
A Marine is attacked and his daughter is kidnapped on Halloween. The team uncovers a scheme involving the blackmail of the girl's mother.
When a Marine is shot on an Army/Navy facility, the team must work with the Army in a joint investigation involving terrorists. Meanwhile, Tony is getting more serious with his girlfriend and the Director is working on a classified project.
When a dead Marine nearly lands on top of the Director at a political function, the team must investigate. Their investigation turns up a second murder victim and they must determine whether their Marine was a murderer or a hero turned victim. Meanwhile, Tony is getting more serious with his girlfriend and Ducky is becoming suspicious of Jimmy and Agent Lee.
McGee's sister shows up on his doorstep covered in blood. When McGee starts investigating to find out what happened, he crosses paths with his team investigating a murder. McGee and the team work to prove his sister didn't kill anyone. Meanwhile, Tony worries about screwing things up with his new girlfriend.
A dead marine in a chimney shoot leads the team to discover a serial killers burial ground. They believe that the dead marine was the serial killer until Abby uncovers something which proves he's another victim. Meanwhile, Tony helps the director with a special project and makes time for his girlfriend as well. And Ducky talks to Gibbs about how he felt betrayed when Gibbs left.
A woman is found dead in a classified robotic vehicle she was working on developing. Although it initially looks like suicide, when Abby puts the vehicle through some tests, it nearly takes her life as well.
A high level Marine intelligence officer found in a small town motel room and the team is called in to investigate. When the team arrives, the discover that the locals have already investigated. As they continue the investigation, the NCIS team discovers that a potential terrorist cell may be involved.
A stoplight rigged to put on an SOS message leads the NCIS team to a dead officer. During the investigation, 10 kilograms of toxic chemical weapons go missing. They discover that wanted terrorist Mamoun Sharif is behind the disappearance as he taunts Gibbs with phone calls.
Ziva and Tony capture an international arms dealer and discovers that the Navy's weapons system is about to be sold to another arms dealer. Ducky goes undercover to meet with the dealer, but there are complications when another agency gets involved as well. Gibbs is concerned that Jenny has a personal vendetta against the dealer.
A man proposing to his girlfriend finds the body of a sailor. NCIS works with local officers believing that the man died of an unintentional drug overdose. However, Abby discovers a message written in blood on a laminated card found at the crime scene. Meanwhile, Jimmy continues his relationship with Agent Michelle Lee.
A Navy Lieutenant arrives at NCIS with radiation poisoning requesting that the team investigate his murder. The Navy Lieutenant is an inspector for the International Atomic Energy Agency, so the team tries to figure out who would want to make sure he didn't make it to the next inspection.
An explosion at a military cemetery mausoleum turns up a skeleton. As they investigate, Ducky discovers that they have turned up the skeleton of more than one body. The team talks to the families to try to find some link between the victims. Meanwhile, Abby is having personal problems.
When the man on Ducky's table turns out to still be alive the unit must track the young marine's actions prior to his arrival in the morgue. They discover that the marine had been on leave and used his time off for a secret trip to Baghdad. The case takes a turn when Gibbs' old commanding officer shows up revealing that the young marine is his son.
Agent Cassidy's NCIS team loses two agents and Gibbs and his team investigate their deaths. They determine that a tip about terrorist activity was actually a trap for the agents. Cassidy forfeits her life to stop a suicide bomber from killing anyone else. Meanwhile, Tony tells his girlfriend he loves her.
McGee is horrified when a Petty Officer on whom he based the character for his latest book is murdered. With little to go on, the team pushes McGee to figure out who could have accessed his secret manuscript.
Jenny is meeting with an informant when he is murdered. Gibbs and the team must try to figure out what information the informant was going to provide about their nemesis and track him down.
With little evidence, the team turns to a blind photographer, Scott to re-create the scene of the crime using his heightened senses of hearing and scent to track down the Petty Officer's killer. Meanwhile, Tony and Gibbs both struggle personal relationships as their girlfriends' push them for a commitment.
Gibbs ignores the bureaucratic paperwork associated with his "acting" director duties and leads an investigation for a murder victim found in a taxi. The team searches for the killer only to discover that he was smuggled into the compound in the cab and the taxi driver was in on it. Meanwhile, Jenny talks to a dying man about La Grenouille and the man claims that he saw her father (who she believed was dead) only a few weeks ago.
As the NCIS Director returns from a controversial European junket, and Gibbs and his agents reluctantly prepare for hastily announced Homeland Security polygraph tests, tightly woven secrets among the team unravel. In addition, an unarmed Dinozzo and his girlfriend are held captive by a merciless drug-dealer.