Season 4, Episode 1: ShalomOriginal Air Date—19 September 2006
Ziva is framed for assassinating an Iranian prisoner and two FBI agents which might result in a diplomatic conflict between the US and Israel governments. Gibbs comes to help her.
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Season 4, Episode 2: EscapedOriginal Air Date—26 September 2006
A bank robber escapes from prison and threatens to kill Fornell's daughter if his case won't be re-opened. Gibbs comes to help.
Season 4, Episode 3: Singled OutOriginal Air Date—3 October 2006
An officer is kidnapped, Tony gets an offer he should not refuse and everybody is freaking out about Gibbs's mustache.
Season 4, Episode 4: Faking ItOriginal Air Date—10 October 2006
The NCIS team is investigating a Russian arms dealer who shot an officer and Gibbs' mentor Mike Franks comes to help.
Season 4, Episode 5: Dead and UnburiedOriginal Air Date—17 October 2006
A marine's body is found inside a new home. The body had been buried, then dug up, and put in the home. His 2 fiancées have been receiving letters from him for the past few months. Did one of them get wise?
Season 4, Episode 6: Witch HuntOriginal Air Date—31 October 2006
On Halloween night a little girl is abducted after her father is attacked. Gibbs and his team must keep searching for the mysterious assailant.
Season 4, Episode 7: SandblastOriginal Air Date—7 November 2006
A marine officer is killed by a bomb on an Army Navy Golf Course. NCIS and Army CID investigate.
Season 4, Episode 8: Once a HeroOriginal Air Date—14 November 2006
A homeless veteran falls from a hotel room into a party with a lot of high ranking officials. During the investigation they discover a body of a young girl who had apparently been assaulted by the veteran.
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Season 4, Episode 9: Twisted SisterOriginal Air Date—21 November 2006
Mc'Gee's restless writing night turns nightmarish when his under-age sister Sara turns up, with bloody hands and a constantly changing story. She's drunk and never could hold her liquor, but is the part she murdered someone without remembering who or why also imagined, or a recollection from a 4 hours black-out? Alas, the fatally stabbed corpse which NCIS investigates on Waverly, her college campus, is that of USS Enterpise seaman Jeff Petty, who dumped Sara for a cheerleader a year earlier. Her cellphone on the corpse puts Gibbs on that trace, and betrays Tim's (dis)loyal silence. She flees, while clues pile up against her or an accident, then returns to the library and gives away Tim's murder novel-writing to the team. Tony has an uncharacteristic dating problem.
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Season 4, Episode 10: SmokedOriginal Air Date—28 November 2006
A body falls out of a smoke stack on a Marine base. The FBI tries to take over the investigation when the body is linked to a serial killer who had vanished. Ducky and Gibbs discuss the source of their conflict.
Season 4, Episode 11: DrivenOriginal Air Date—12 December 2006
A Navy Lieutenant dies from carbon monoxide poisoning while testing a prototype vehicle. At first it looks like suicide, but NCIS determines that it was murder.
Season 4, Episode 12: SuspicionOriginal Air Date—16 January 2007
When a high-level Marine intelligence officer is found murdered in a small motel room, the NCIS team must find the person who murdered her. After discovering that the person was dead for already three days, and that the town authorities already "investigated" the crime, Gibbs is determined to solve the case, which could be related to a terrorist cell, and not let the town authorities get in his way.
Season 4, Episode 13: Sharif ReturnsOriginal Air Date—23 January 2007
Sharif the terrorist responsible for planting the bomb in Sandblast is back. Now he's using chemical weapons. A marine is found an apparent victim/test subject for Sharif's latest scheme.
Season 4, Episode 14: BlowbackOriginal Air Date—6 February 2007
The secret mission that Jen's been using Tony for finally pans out. She's been pursuing her suspect for a decade. But they'll need the rest of the team, and Ducky to complete the mission.
Season 4, Episode 15: Friends & LoversOriginal Air Date—13 February 2007
A dead marine leads the team to a Night Club, and a search for a possible serial killer. Gibbs and the Metro Police clash over jurisdiction, and protocols.
Season 4, Episode 16: Dead Man WalkingOriginal Air Date—20 February 2007
A navy lieutenant walks into NCIS and asks Gibbs to solve his own murder. He has been poisoned by radiation. While the team investigates, Ziva tries to figure out why the man seems so familiar to her.
Season 4, Episode 17: SkeletonsOriginal Air Date—27 February 2007
Some maintenance workers open a crypt, and it explodes. They find some skeletons in what was supposed to be an empty unit. Ducky finds out there multiple skeleton parts, NCIS must track down a serial killer.
Season 4, Episode 18: IcemanOriginal Air Date—20 March 2007
Just as Ducky is about to perform an autopsy, his patient wakes up on the table. NCIS investigates Gibbs finds out an old friend has a personal stake in the matter. Tony's relationship hits a cross roads.
Season 4, Episode 19: Grace PeriodOriginal Air Date—3 April 2007
Cassidy's team gets a tip on a terrorist plot, when they investigate. The agents are killed by a suicide bomber. Cassidy teams with Gibbs' team to find out who set up her agents. Ducky and Abby find evidence that seems to contradict each other. Gibbs reveals a secret to his team that affects some of his agents.
Season 4, Episode 20: Cover StoryOriginal Air Date—10 April 2007
While processing evidence from a crime scene, McGee is shocked when he discovers a link to his newest/unfinished novel. When the team finds 2 bodies, the race is on to find the killer and his link to McGee's work. McGee finally admits he based his characters off his co-workers.
Season 4, Episode 21: Brothers in ArmsOriginal Air Date—24 April 2007
Jenny finds a person who's willing to give her evidence of La Grenouille's activities. But her informant is killed. Her behavior is becoming more obsessive, while Gibbs and his team try to help her.
Season 4, Episode 22: In the DarkOriginal Air Date—1 May 2007
A blind photographer takes a picture of a dead sailor. Gibbs and his team must find clues from his other photographs, and from other leads provided by the photographer.
Season 4, Episode 23: Trojan HorseOriginal Air Date—8 May 2007
When Director Shepherd goes out of country, Gibbs steps in as acting Director. That doesn't preclude him from heading an investigation into the death of a person who was on his way to NCIS.
Season 4, Episode 24: Angel of DeathOriginal Air Date—22 May 2007
Director Shepard returns and finds evidence that someone from her past may still be alive. NCIS must undergo polygraph tests, ordered by Homeland Security. While Gibbs investigates who ordered the tests, Tony and Jeanne face a crisis together.