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- Season 3 overviewSep 20, 2005-May 16, 200624 episodesSeason 3 episodes24. Hiatus May 16, 2006
- Gibbs suffers a temporary memory loss as he recovers; the team tries to prevent a terrorist attack.
- 23. Hiatus May 9, 2006
- Gibbs' long-suppressed memories overwhelm him as he recovers from injuries.
- 22. Jeopardy May 2, 2006
- Ziva finds herself under investigation for the death of a suspect; Director Shepard is kidnapped.
- 21. Bloodbath Apr 25, 2006
- Abby becomes the target of a stalker, sending the team into protective overdrive.
- 20. Untouchable Apr 18, 2006
- Gibbs and his team must investigate the apparent suicide of a Pentagon cryptographer.
- 19. Iced Apr 4, 2006
- Gibbs and the team investigate when the body of a missing Marine is found in a frozen lake.
- 18. Bait Mar 14, 2006
- A high schooler on Quantico Marine Corps Base attaches a bomb to himself and holds students hostage.
- 17. Ravenous Mar 7, 2006
- The team searches for Marine who went missing in a national forest.
- 16. Family Secret Feb 28, 2006
- An ambulance explodes while transporting the remains of a Marine.
- 15. Head Case Feb 7, 2006
- The team busts an illegal automotive chop-shop run by Marines.
- 14. Light Sleeper Jan 24, 2006
- When the wives of two Marines are murdered, the team fears the murders are racially motivated.
- 13. Deception Jan 17, 2006
- The commander in charge of a shipment of nuclear weapons seems to have been abducted.
- 12. Boxed In Jan 10, 2006
- Tony and Ziva become trapped while investigating weapons smuggling.
- 11. Model Behavior Dec 13, 2005
- Gibbs and his team uncover a twisted love triangle as they hunt for the killer of a murdered model.
- 10. Probie Nov 29, 2005
- The team works to clear McGee's name when he kills an undercover police officer while on assignment.
- 9. Frame-Up Nov 22, 2005
- Tony is suspected of murder when part of a female body is found at Quantico.
- 8. Under Covers Nov 8, 2005
- When the bodies of two assassins are delivered to NCIS, Tony and Ziva go under cover.
- 7. Honor Code Nov 1, 2005
- An officer working as the Navy's liaison with a defense contractor is reported missing.
- 6. The Voyeur's Web Oct 25, 2005
- Two bored housewives begin running an Internet sex site from their bedrooms.
- 5. Switch Oct 18, 2005
- A petty officer with a double life is gunned down on a freeway.
- 4. Silver War Oct 11, 2005
- A dead staff sergeant is found encased in a Civil War-era tomb; clues lead to a safety deposit box.
- 3. Mind Games Oct 4, 2005
- Gibbs must meet with a serial killer days before his execution.
- 2. Kill Ari Sep 27, 2005
- Ari continues to wreak havoc on the team until Gibbs gets the face-off he has been awaiting.
- 1. Kill Ari Sep 20, 2005
- The team works to collect all the evidence they can in an effort to stop Ari.