NCIS (season 3)

As the team struggles to cope with Kate Todd's sudden and unexpected death, Gibbs clashes with the new NCIS Director Jenny Shepard, who believes that Ari Haswari was not the one responsible for firing the bullet that killed Agent Todd. Ziva David, Ari's Mossad control officer, sides with the director, and causes problems when she arrives in the NCIS office. However, Ziva's motives for defending Ari become murky when she communicates with him and does not tell anyone in the NCIS office. Ari kidnaps Ducky to divert the team's attention away from Ziva.

Recurring characters: Alan Dale as Director Morrow, Pancho Demmings as Gerald Jackson, Lauren Holly as Director Shepard and Rudolf Martin as Ari Haswari.
Note: First allusion to Gibbs' first family

Gibbs's determination to kill Ari increases after he mounts attacks against various members of the team in his sadistic game with Gibbs. Ari's control officer, Ziva David, begins to doubt Ari's innocence and agrees with Gibbs' plan to present Ari with the opportunity to kill him. It is only after the encounter between the three of them, that Gibbs discovers why Ziva was so quick to defend the murderer: she and Ari are in fact half-siblings. The team bids a sad farewell to Todd as she is laid to rest with civilian honors. NCIS Director Morrow approved Gibbs's request that Todd be awarded the Presidential Medal of Freedom.

Recurring characters: Joe Spano as FBI Agent Fornell, Pancho Demmings as Gerald Jackson, Lauren Holly as Director Shepard and Rudolf Martin as Ari Haswari.

Death row prisoner Kyle Boone is a serial killer whom Gibbs arrested ten years ago. Having been placed on Death Row and due to executed in a few days time, he insists that he will disclose the location of the missing bodies of his murder victims to Gibbs alone, forcing the reluctant team leader to meet with him. When Abby and McGee locate the place where the victims had been murdered, the team, assisted by Agent Cassidy, finds that the latest four victims in Boone's scrapbook had been killed in the last three years, meaning Boone has an accomplice. When Agent Cassidy goes missing, the team is forced into a desperate race against time to prevent her from becoming victim number five of the copycat killer.

A deceased Marine is found encased in a Civil-War era tomb at the Smithsonian museum. In the meantime, Ziva David joins NCIS as a liaison officer for Mossad and is assigned by the new director of NCIS, Jenny Shepard to Gibbs's team without his consent. She is forced to prove her worth to the team as they track down the people responsible for the Staff Sergeant's death, which is linked to a Civil War treasure. When Ducky and Ziva are placed in a difficult position, Ziva shows her value by saving both their lives.

The team is called to investigate the murder of a Petty Officer who was gunned down while driving on a freeway. While visiting the sailor's commander to inform him of the death, the team discovers that another man claims to be the Petty Officer and that his identity may have been stolen. Secrets in both men's lives are revealed, but it is shrewd observations by Abby that end up solving the case.

Jamie Carr, a Marine Sergeant's wife, is thought to have been abducted until Gibbs and his team found evidence to suggest that she may have been murdered live on the internet. Carr and her neighbor, Leanne Roberts, had been making money by running a live internet sex site while their husbands' were deployed abroad. Roberts's body is later found but the team is still unable to find any trace of Carr. With the help of her new assistant, Charles Sterling, Abby determines that the video of Jamie might not be all it seems.

Recurring characters: Brian Dietzen as Jimmy Palmer, Lauren Holly as Director Shepard, Stephanie Mello as Cynthia and Michael Bellisario as Charles "Chip" Sterling.

Gibbs befriends a young boy after his father, a Lt. Commander, is kidnapped. The Lt. Commander had been working on a classified project named Honor and is the only person who has the code keys to the project. The release of the code keys can pose a serious threat to national security. Although the evidence gathered by Gibb's team suggests that the Lt. Commander was a part of the scheme, Gibbs believes otherwise due to the strong bond between the Lt. Commander and his son.

When it is discovered that two married assassins, who were fatally wounded in a car crash, were planning an assassination at the United States Marine Corps Birthday Ball, Gibbs sends Ziva and Tony to pose as the married assassins in order to find out who the couple had planned to assassinate and who had hired them. After the team finds out that the couple were expecting a baby and may have been planning to retire, they realize that the assassination plot could have been a set-up and that the married assassins were potentially the real targets. Meanwhile, an attraction between Tony and Ziva surfaces.

A pair of legs are found on a Marine base, and the team is dumbfounded and shellshocked when every piece of evidence in a murder points towards Tony as the prime suspect. In an effort to help their colleague, the team compiles a list of people who may have grudges against Tony, providing them with a long list of suspects. Abby is upset that she may have incriminated Tony through the forensic evidence she provided and refuses to give up until she's proved his innocence.

Recurring characters: Brian Dietzen as Jimmy Palmer, Joe Spano as FBI Agent Fornell and Michael Bellisario as Charles "Chip" Sterling.

While the team is on protective detail for the Chief of Naval Operations, McGee spots an argument taking place in an alleyway. He shoots one of the men, who he believed was aiming a gun at him. The deceased turns out to be a D.C. Metro police detective who was working undercover. When the team is unable to find any weapon or bullets left behind by anyone other than McGee, it appears that McGee may have made a probie mistake. McGee begins to doubt himself but Gibbs is suspicious of the detective's meeting, which took place that night. After speaking to the decedent's partner, the team realizes that McGee's story may be more accurate than any of them thought.

A supermodel is found dead after having overdosed on phencyclidine at a Marine base, where the reality TV show in which she was participating was being filmed. Her ex-boyfriend is also found dead in a motel nearby having overdosed on heroin, leading the team to believe that their deaths may have been related to their relationship. However, when it is discovered that the Marine drill instructor in charge of the TV show was romantically linked to the dead supermodel, the team look closer at the others involved in the show. When the Marine boyfriend begins to overdose on the same thing that killed his girlfriend, it appears that someone may have disapproved of the relationship, going to extreme lengths to end it.

When the Korean wives of two Marines are murdered, Gibbs and his team are sent in to investigate. Since signs of domestic abuse were evident at the crime scene, they suspect that the killer is one of the women's husbands. The sudden disappearance of Yoon Dawson, a friend of the two victims, makes her husband a suspect in the case. However, the team soon discovers that Yoon is not all she seems, and that she and her two dead friends might have been in America for reasons other than having Marine husbands.

While conducting a raid on an automotive chop shop run by Marines, the team finds a severed head in one of the cars. The head belonged to a Navy Captain, who was thought to have been cremated. Their investigation leads them to the discovery of a scheme involving the illegal sale of human body parts, which came from stolen bodies.

An ambulance explodes and practically disintegrates the body of William Danforth, a deceased Marine it was carrying. A DNA analysis performed on a piece of body tissue informs the team that the body does not belong to Danforth. The team suspects that Danforth's best friend, who was a bomb expert, helped Danforth fake his death in order to leave the Marine Corps. When Danforth is discovered to have been a recipient of a donor organ, the team realizes that the body may in fact be Danforth's after all, and they are forced to examine reasons as to why someone may have wanted to disguise that the body was his.

A Marine is suspected to have been eaten by a bear after a group of teenagers found his dog tags in bear feces in a national forest. However, autopsy reveals that the Marine was killed by a blade before his corpse was eaten by a bear. Evidence also shows that he was camping with a woman, who is now missing. The team's search for the woman and the Marine's killer leads them to a realization that their case may be linked to several women of similar appearance who have been found dead in the national forest. The team realizes that locals may know more than they have been telling.

The teenage son of a Marine Major holds his classmates hostage inside a classroom by threatening them with a bomb strapped to his chest. Gibbs and his team arrive on scene but are unable to get audio and video of the situation inside the classroom so Gibbs puts himself in danger by offering himself as a hostage. While Tony takes charge of the team, the boy demands that his mother be brought to the classroom by sunset, but the team discovers that she has been dead for a year. Gibbs suspects that the boy is not acting alone when he sees an earwig in the boy's ear.

NCIS is called to investigate a dead Marine First Sergeant found in a frozen lake. The discovery of three more dead men in the lake leads Gibbs to the underworld of an international street gang, which may threaten the safety of the team. The team finds a link between the dead men and a one-year-old case concerning the accidental shooting of a Marine by the gang.

Due to suspicions of a mole working inside the Pentagon, Tony and Ziva are charged with interviewing members of the Pentagon's cryptography department. When one of their interviewees is found dead in her home, the team investigates her apparent suicide. While the cryptography department is immediately locked down, Abby uses forensic science to prove that a second person was in the room when the gun was fired.

After a room at a Navy lodging facility is found to have blood and fragments of flesh scattered throughout, the team is called to investigate. However, evidence suggests that it was a set-up crime scene. Meanwhile, Abby returns from court after giving testimony in an embezzlement trial and is attacked in her lab. Gibbs puts Abby into protective custody with the team while they look for the person targeting Abby, who appears to be a stalker. It was discovered that the defendant in the trial had used some of the ill-gotten money to hire a hit man to target Abby. It was Abby, who had been armed with pepper spray, brass knuckles and a taser gun, who had subdued the hit man, and helped to get the defendant arrested.

NCIS investigates the death of a suspect who was in Ziva's custody but the investigation turns critical when the dead man's brother kidnaps Director Shepard and threatens to kill her unless the seized evidence and his brother are returned, unaware that his brother is actually dead. While Ducky works to find the man's cause of death, the team desperately searches for their Director.

A bomb explodes as Gibbs contacts an undercover government agent on a suspicious foreign ship, killing the agent and placing Gibbs in a coma, in which he has flashbacks of the murder of his wife and daughter many years earlier, and his wounding in Desert Storm. Meanwhile, Tony becomes the temporary head of the investigation team as the group attempts to track down Pinpin Pula, a missing crew member of the ship, suspected to be an Abu Sayyaf member. Gibbs awakens from his coma at the end of the episode with no memory of Ducky, who is in the room with him.

Shepard contacts Gibbs's NCIS mentor and partner, Mike Franks in hopes of helping an amnesiac Gibbs regain his memory as only he knows the details to an impending terrorist attack. Ziva, who had appeared nonchalant about Gibbs's situation, visits Gibbs in a desperate and emotional attempt to revive his memory by telling him about their shared connection with Ari. Meanwhile, Tony and the team discover Pinpin Pula wants to blow up the ship Cape Fear. Gibbs recovers his memory and tries to stop the terrorist attack, but fails because his superiors ignore his warnings. Finally, Gibbs hands his badge to Tony and resigns before heading to Mexico to stay at Franks's house.

Recurring characters: Brian Dietzen as Jimmy Palmer, Stephanie Mello as Cynthia and Muse Watson as Mike Franks.