While the NCIS team deals with Kate's death, Gibbs' determination to finally put an end to Ari's reign of terror mounts.
Ari continues to wreak havoc on the NCIS team as he uses its members as pawns in the game he is playing with Gibbs.
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.
Gibbs and the team are called in when a recently deceased man is found encased in a Civil War-era tomb.
The NCIS team is called in when a Petty Officer is brutally gunned down on the freeway.
Gibbs and the team investigate the murder of Marine's wife that appears to have been broadcast over the Internet.
Gibbs and the team investigate when a 6-year-old boy informs NCIS his father has been kidnapped.
When the bodies of two assassins are delivered to NCIS from overseas, Tony and Ziva assume their identities undercover and engage in a sexy rendezvous at a luxury hotel in order to find their target.
The NCIS team rallies to clear his name when Tony is accused of murder.
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.
Gibbs and the team investigate the murder of a supermodel filming a reality TV show on a Marine base.
Gibbs and the team rush to find Tony and Ziva who disappear while investigating a shipyard for smuggled weapons.
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.
When the wives of two Marines are murdered, Gibbs and the team are called in to investigate.
Gibbs and the NCIS team make a disturbing discovery when they bust an illegal automotive chop shop run by Marines.
The team investigates the mysterious explosion of an ambulance that is supposedly carrying the remains of a Marine killed in a car crash.
Gibbs and the team are called to investigate when a group of teens on a nature hike discover Marine dog tags in a national forest.
Gibbs and the team are called in when a teenage student at a Quantico base high school attaches a bomb to his body and holds his fellow students hostage.
Gibbs and the team are called in when a couple of kids stumble upon the body of a missing Marine in a frozen lake.
Gibbs and the team are called in when a Pentagon cryptographer suspected of spying apparently commits suicide.
Gibbs and the team go into protective overdrive when Abby becomes the prey of a stalker.
Ziva becomes the focus of an NCIS investigation when a suspect in her custody dies.
The NCIS is distressed when Gibbs is injured in a terrorist explosion while on assignment in part one of a two part third season finale.
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.