Writer: William Webb
Director: John C. Kelley, Donlad P. Bellisario
Air Date: 09/19/06
Synopsis:With Gibbs retired and boat-building in Mexico, the NCIS team must learn to work without him when Ziva is wanted by the FBI after she witnesses a political assassination
Writer: Dennis Smith
Director: Steven D. Binder, Christopher Sibler
Air Date: 09/26/06
Synopsis: Gibbs is temporarily reinstated at NCIS when his friend's life is threatened by an escaped convict.
Writer: Terrence O'Hara
Director: David North
Air Date: 10/03/06
Synopsis: The NCIS team is called to investigate a bloody, abandoned car registered to a missing Navy lieutenant.
Writer: Shane Brennan
Director: Thomas J. Wright
Air Date: 10/10/06
Synopsis: Gibbs and the team investigate when the body of a Petty Officer is found in a car shot at close range.
Writer: Nell Scovell
Director: Colin Bucksey
Air Date: 10/17/06
Synopsis: The NCIS team is called to investigate when a real estate agent finds the body of a missing Lance Corporal is found in a vacant house.
Writer: Steven Kriozere
Director: James Whitmore, Jr.
Air Date: 10/31/06
Synopsis: Gibbs and the NCIS team investigate when a Marine is attacked in his home and his daughter is apparently kidnapped on Halloween night.
Writer: Robert Palm
Director: Dennis Smith
Air Date: 11/07/06
Synopsis: When an explosion kills a Marine Colonel on a military golf course, the NCIS team must work together with the Army Criminal Investigative Unit to find the killer.
Writer: Shane Brennan
Director: Thomas J. Wright
Air Date: 11/14/06
Synopsis: When suspicious activity surrounds the death of a decorated Marine veteran, the NCIS team works to clear his name.
Writer: Steven D. Binder
Director: Terrence O'Hara
Air Date: 11/21/06
Synopsis: McGee breaks the rules, risking his NCIS job, to help his sister Sara, who showed up disoriented and bloodied.
Writer: John C. Kelley, Robert Palm
Director: Dennis Smith
Air Date: 11/28/06
Synopsis: When a burnt and mummified body of a missing and wanted person is found on a Marine base, in a furnace, NCIS must work with FBI.
Writer: Dennis Smith
Director: John C. Kelley, Richard Arthur
Air Date: 12/12/06
Synopsis: A highly classified robotic vehicle causes the death of a Navy lieutenant working on a high-level project for the Department of Defense; Tony's secretive trips to the hospital worry Ziva.
Writer: Shane Brennan
Director: Colin Bucksey
Air Date: 01/16/06
Synopsis: The team battles local biases when it investigates the murder of a high-level Marine intelligence officer found in a small-town motel room.
Writer: Steven D. Binder
Director: Terrence O'Hara
Air Date: 01/23/06
Synopsis: The NCIS team must track down a wanted terrorist who has obtained a missing, highly toxic chemical weapon. Susanna Thompson guest stars.
Writer: Christopher Sibler
Director: Thomas J. Wright
Air Date: 02/06/06
Synopsis: Ducky goes under cover to stop the illegal sale of the Navy's top-secret weapons system to a high-priority arms dealer (Armand Assante).
Writer: John C. Kelley
Director: Dennis Smith
Air Date: 02/13/06
Synopsis: When a young sailor's body is found in an abandoned building in a seedy part of time, an ominous message written in blood leads the team to switch gears to find the killer.
Writer: Nell Scovell
Director: Colin Bucksey
Air Date: 02/20/06
Synopsis: The NCIS team suspects foul play when a Navy lieutenant is the victim of radiation poisoning; Tony sees a softer side of Ziva.
Writer: Jesse Stern
Director: James Whitmore, Jr.
Air Date: 02/27/06
Synopsis: Gibbs and the team look for a potential serial killer when an explosion at a military cemetery mausoleum reveals a cache of dismembered human remains.
Writer: Shane Brennan
Director: Thomas J. Wright
Air Date: 03/20/06
Synopsis: With the young Marine on life support, the NCIS team tracks his movements in the days before he was left for dead and discovers a secret trip to Baghdad via a private cargo plane and a link to Gibbs' past.
Writer: John C. Kelley
Director: James Whitmore, Jr.
Air Date: 04/03/06
Synopsis: Cassidy (Jessica Steen) blames herself when the team learns that a tip on terrorist activity was a trap that resulted in the deaths of two agents.
Writer: David North
Director: Dennis Smith
Air Date: 04/10/06
Synopsis: When a petty officer on whom McGee based a character for his latest book is murdered, McGee must figure out who could have accessed his secret manuscript.
Writer: Steven D. Binder
Director: Martha Mitchell
Air Date: 04/24/06
Synopsis: Director Shepard takes a huge risk and agrees to meet an informant alone, but the meeting goes bad and her contact is killed. Gibbs and the NCIS team attempt to gather the information the man was going to supply or risk losing their nemesis once again.
Writer: Steven D. Binder
Director: Thomas J. Wright
Air Date: 05/01/06
Synopsis: With little evidence, the team turns to 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 struggle with personal relationships.
Writer: Shane Brennan, Donald P. Bellisario
Director: Terrence O'Hara
Air Date: 05/08/06
Synopsis: Gibbs ignores the bureaucratic paperwork associated with his "acting" director duties and leads an investigation for a murder victim found in a taxi headed to NCIS headquarters. Meanwhile, Jenny discovers a secret about her past.
Writer: Donald P. Bellisario
Director: Terrence O'Hara
Air Date: 05/22/06
Synopsis: 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.
