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- Season 6 overviewSep 23, 2008-May 19, 200925 episodesSeason 6 episodes25. Aliyah May 19, 2009
- Ziva has a tense reunion with her father, the head of Mossad.
- 24. Semper Fidelis May 12, 2009
- The team works with ICE and FBI agents when a security breach leads to the death of an ICE agent.
- 23. Legend May 5, 2009
- Tony questions Ziva's loyalty to NCIS; Special Agent Callen goes under cover.
- 22. Legend Apr 28, 2009
- The murder of a Marine brings McGee and Gibbs to Los Angeles.
- 21. Toxic Apr 7, 2009
- When a government scientist goes missing, Abby is asked to step in.
- 20. Dead Reckoning Mar 31, 2009
- Gibbs reluctantly works with Trent Kort to put away one of the department's most-wanted criminals.
- 19. Hide and Seek Mar 24, 2009
- A military family comes under suspicion when a boy finds a murder weapon.
- 18. Knockout Mar 17, 2009
- A boxer's death leads to Vance starting his own investigation; Gibbs looks into Vance's past.
- 17. South by Southwest Feb 24, 2009
- Gibbs and Tony try to locate a woman who might have answers about an agent's murder.
- 16. Bounce Feb 17, 2009
- A murder prompts the reopening of one of Tony's old investigations.
- 15. Deliverance Feb 10, 2009
- Gibbs finds a cryptic message waiting for him at a crime scene.
- 14. Love & War Jan 27, 2009
- The team discovers a link between a sergeant's murder and his possibly treasonous private life.
- 13. Broken Bird Jan 13, 2009
- Ducky is stabbed at a crime scene, and the team uncovers disturbing secrets from the doctor's past.
- 12. Caged Jan 6, 2009
- McGee is held captive in a women's prison after a guard's murder leads to a takeover.
- 11. Silent Night Dec 16, 2008
- The team is forced to put in overtime while searching for a suspect presumed dead.
- 10. Road Kill Dec 2, 2008
- The team investigates the death of a petty officer who may have been leading a violent secret life.
- 9. Dagger Nov 25, 2008
- The team is forced to rely on information from questionable sources while trying to stop a criminal.
- 8. Cloak Nov 18, 2008
- The team must play a dangerous war game that leads to very real consequences for one team member.
- 7. Collateral Damage Nov 11, 2008
- Vance assigns a rookie to work with Gibbs on the team's investigation into a deadly bank robbery.
- 6. Murder 2.0 Oct 28, 2008
- A murderous psychopath taunts the team by leaving clues to the next victim's identity.
- 5. Nine Lives Oct 21, 2008
- Gibbs' hunt for the killer of a marine puts him on a collision course with an old friend.
- 4. Heartland Oct 14, 2008
- When a murder investigation leads the team to Gibbs' hometown, secrets about his past are revealed.
- 3. Capitol Offense Oct 7, 2008
- A distinguished senator asks Gibbs for help in solving the murder of a young female Naval officer.
- 2. Agent Afloat Sep 30, 2008
- DiNozzo's investigation into a suicide takes a surprising and deadly turn.
- 1. Last Man Standing Sep 23, 2008
- Gibbs finds a shocking connection between a murder and the director's decision to disband his team.