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"Kill Ari I"
Episode 47

Writer: Donald P. Bellisario
Director: Dennis Smith
Air Date: 09/20/05

Synopsis: While the NCIS team deals with Kate's death, Gibbs' determination to finally put an end to Ari's (Rudolf Martin) reign of terror mounts.

"Kill Ari II"
Episode 48

Writer: Donald P. Bellisario
Director: James Whitmore, Jr.
Air Date: 09/27/05

Synopsis: When Ari kidnaps a member of the team, Gibbs goes on a frantic search for his colleague and friend.

"Mind Games"
Episode 49

Writer: George Schenck, Frank Cardea
Director: William Webb 
Air Date: 10/04/05

Synopsis: Gibbs is ordered to meet with a convicted serial killer three days away from his execution in order to find out crucial information before he dies.

"Silver War"
Episode 50 

Writer: Terrence O'Hara 
Director: John C. Kelley 
Air Date: 10/11/05

Synopsis: Gibbs and the team are called in when a recently deceased man is found encased in a Civil War-era tomb.

"Switch"
Episode 51

Writer: Gil Grant 
Director: Thomas J. Wright 
Air Date: 10/18/05

Synopsis: The NCIS team is called in when a Petty Officer is brutally gunned down on the freeway.

"The Voyeur's Web"
Episode 52

Writer: David North 
Director: Dennis Smith 
Air Date: 10/25/05

Synopsis: Gibbs and the team investigate the murder of a Marine's wife that appears to have been broadcast over the Internet.

"Honor Code"
Episode 53

Writer: Christopher Sibler 
Director: Colin Bucksey 
Air Date: 11/01/05

Synopsis: Gibbs and the team investigate when a 6-year-old boy informs NCIS his father has been kidnapped.

"Under Covers"
Episode 54

Writer: Lee David Zlotoff 
Director: Aaron Lipstadt 
Air Date: 11/08/05

Synopsis: When the bodies of two assassins are delivered to NCIS from overseas, Tony and Ziva go undercover in order to find their targets.

"Frame Up"
Episode 55

Writer: Laurence Walsh 
Director: Thomas J. Wright 
Air Date: 11/22/05

Synopsis: The NCIS team rallies to clear his name when Tony is accused of murder

"Probie"
Episode 56

Writer: George Schenck, Frank Cardea
Director: Terrence O'Hara 
Air Date: 11/29/05

Synopsis: When McGee kills a man while on assignment, the NCIS team steps in to back him when they discover the man was an undercover police officer

"Model Behaviour"
Episode 57

Writer: David North 
Director: Stephen Cragg 
Air Date: 12/13/05

Synopsis: Gibbs and the team investigate the murder of a supermodel filming a reality TV show on a Marine base, uncovering a twisted love triangle. 

"Boxed In"
Episode 58

Writer: Dana Coen 
Director: Dennis Smith 
Air Date: 1/10/06

Synopsis: While searching a Senegalese ship that they believe is being used to smuggle small arms, Tony and Ziva are captured and locked in a container while the team tries to discover their whereabouts.

"Deception"
Episode 59

Writer: Jack Bernstein 
Director: Leslie Libman 
Air Date: 1.17/06

Synopsis: Gibbs and the team are called in on a weekend when a Navy Lt. Commander in charge of a shipment of nuclear weapons is apparently abducted

"Light Sleeper"
Episode 60

Writer: Christopher Sibler 
Director: Colin Bucksey 
Air Date: 1/24/06

Synopsis: When the wives of two Marines are murdered, the team fears the murders are racially motivated and works together to find the killer

"Head Case"
Episode 61

Writer: George Schenck, Frank Cardea
Director: Dennis Smith 
Air Date: 2/07/06

Synopsis: Gibbs and the NCIS team make a disturbing discovery when they bust an illegal automotive chop shop run by Marines.

"Family Secret"
Episode 62

Writer: Steven D. Binder
Director: James Whitmore, Jr.
Air Date: 2/28/06

Synopsis: The team investigates the mysterious explosion of an ambulance that is supposedly carrying the remains of a Marine killed in a car crash,

"Ravenous"
Episode 63

Writer: Richard C. Arthur 
Director: Thomas J. Wright 
Air Date: 3/07/06

Synopsis: Gibbs and the team are called to investigate when a group of teens on a nature hikers discover Marine dog tags in a national forest.

"Bait"
Episode 64

Writer: Laurence Walsh
Director: Terrence O'Hara
Air Date: 3/14/06

Synopsis: The NCIS team must stop a teenage student from detonating a bomb attached to his body, while he's taking the other students hostage at a Quantico base high school.

"Iced"
Episode 65

Writer: Dana Coen 
Director: Dennis Smith 
Air Date: 4/04/06

Synopsis: Gibbs and the team are called in when a couple of kids stumble upon the body of a missing Marine in a frozen lake

"Untouchable"
Episode 66

Writer: George Schenck, Frank Cardea
Director: Leslie Libman 
Air Date: 4/18/06

Synopsis: Gibbs and the team are called in when a Pentagon cryptographer suspected of spying apparently commits suicide.

"Bloodbath"
Episode 67

Writer: Steven D. Binder 
Director: Dennis Smith 
Air Date: 4/25/06

Synopsis: Gibbs and the team go into protective overdrive when Abby becomes the prey of a stalker.

"Jeopardy"
Episode 68

Writer: David North 
Director: James Whitmore, Jr.
Air Date: 5/02/06

Synopsis: Ziva finds herself under investigation when a suspect in her custody dies.

"Hiatus part 1"
Episode 69

Writer: Donald P. Bellisario
Director: Dennis Smith 
Air Date: 5/09/06

Synopsis: Gibbs Is Injured In a Terrorist Explosion.Tony steps into the role of senior agent, causing a bit of resentment from other team members. Meanwhile, while recovering, Gibbs is flooded with memories of his past that he had long struggled to suppress. IN PART ONE OF A TWO PART THIRD SEASON FINALE

"Hiatus part 2"
Episode 70

Writer: Donald P. Bellisario
Director: Dennis Smith 
Air Date: 5/16/06

Synopsis: While Gibbs recovers from an injury caused by a bomb explosion, he experiences temporary memory loss, while his team tries to stop a terrorist group from carrying out a devastating attack on the Navy. IN THE SECOND HOUR OF THE THIRD SEASON FINALE