While the NCIS team deals with Kate's death, Gibbs' determination to finally put an end to Ari's (guest star Rudolf Martin) reign of terror mounts. Lauren Holly ("Chicago Hope") joins the cast as the new Director of NCIS who has a romantic history with Gibbs. Cote de Pablo ("The Street") joins as a new NCIS agent that spars with Tony. Though he has no concrete evidence that the sniper was Ari, Gibbs is haunted by the thought that the bullet that killed Kate was meant for him. As the team works to collect all the evidence they can in an effort to stop Ari, each of them is forced to confront their emotions about Kate's violent death. Meanwhile, the director of NCIS informs Gibbs he will be leaving to take on a new position and introduces him to his new boss, Jenny Shepard (Lauren Holly), a woman with whom Gibbs has a sordid past.

Ari (guest start Rudolf Martin) continues to wreak havoc on the NCIS team as he uses its members as pawns in the game he is playing with Gibbs. Gibbs, who is still haunted by images of Kate's death, is determined to stop Ari after he and Director Shepard are the target of sniper fire and Ducky is lured out of the NCIS headquarters by the terrorist. Though Gibbs is still uncertain of Ziva's connection to Ari, she becomes an invaluable asset when Gibbs finally comes face to face with his arch nemesis.

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. Under order from the Governor of Virginia, a skeptical Gibbs is forced to meet with a serial killer he helped to convict a decade before under the pretense that the killer will tell Gibbs where he hid missing bodies and give closure to the families before his death. Gibbs' instinct is correct when the killer is coy and doesn't reveal what he promised. Nonetheless, Gibbs has an NCIS team in place to re-investigate the possible locations of the victims. When a crucial piece of information is discovered, Abby and McGee use their expertise to attempt to pinpoint where the bodies might be.

Gibbs and the team are called in when a recently deceased man is found encased in a Civil War-era tomb. Gibbs and the team discover that the corpse inside the cast-iron tomb is that of a missing Staff Sergeant who, according to Ducky, was buried alive. Using cell phone records from a phone found inside the casket, Abby tracks the victim's final phone calls to a bank and safety deposit box that contains a map the Staff Sergeant died protecting. Meanwhile, Director Shepard informs Gibbs that Agent David will now be a full-time member of his team.

The NCIS team is called in when a Petty Officer is brutally gunned down on the freeway. As the investigation unfolds, Gibbs and the team discover that the Petty Officer had been living a double life and had switched identities with a former colleague whose job of illegal transporting gives the team their first lead to the murderer. But the break in the case is shortlived when Abby uncovers a message the Petty Office left before dying that leads them in an entirely different direction.

Gibbs and the team investigate the murder of Marine's wife that appears to have been broadcast over the Internet. The NCIS team discovers that two bored housewives, whose husbands are serving in Iraq, have been running an Internet sex site from their bedrooms. With both women now missing and an Internet file of what appears to be a murder, Gibbs and the team decide to track down the webmaster and follow the money in order to locate the murderer.

Gibbs and the team investigate when a 6-year-old boy informs NCIS his father has been kidnapped. Gibbs quickly develops a unique bond with the young boy whose missing father is a Lt. Commander working as the Navy's liaison with a defense contractor on a highly confidential project called "Honor." The NCIS team discovers that the top-secret program, for which the missing Commander holds the only code, has been hacked and classified data has been removed. As the evidence begins to indicate the kidnapping may be a hoax, Gibbs holds his ground when his gut tells him the Lt. Commander is innocent.

Simone and IAB share the suspect after Bobby gets some information from his incarcerated friend, Ray, about a case that Mike Roberts once worked. Fancy and Sipowicz both work the case of a self-confessed gunman in a neighborhood shooting, once they get the story they help the shooter out. Medavoy investigates the assault case of an actor who was injured in staged fight that went awry.

David Brant, Director of the real NCIS in Washington, D.C., guest stars as an NCIS Agent. The NCIS team rallies to clear his name when Tony is accused of murder. When a portion of a female body is found at Quantico, the NCIS team investigates and is shocked to discover that all the forensic evidence points to Tony as the prime suspect. As Abby questions her faith in her science and her ability as a specialist, she makes it her personal mission to prove Tony's innocence and find out who is trying to frame him for murder before it's too late.

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 is furious when Director Shepard overrules him and allows the police to run their own investigation on McGee. Determined to clear McGee's name and prove his actions were justified, the NCIS team bands together to protect one of their own. Meanwhile, Tony gets a troublesome phone call from his past.

Gibbs and the team investigate the murder of a supermodel filming a reality TV show on a Marine base. At the start of the investigation, the team believes the model may have committed suicide, but they uncover a twisted love triangle involving the Marine staff sergeant working on "Boot Camp Babes," a drug addicted ex-boyfriend and a disgruntled adoptive father, who is also the executive producer of the reality show. Meanwhile, Director Shepard is annoyed when Gibbs doesn't show up at an awards ceremony where he is being honored.

Gibbs and the team rush to find Tony and Ziva who disappear while investigating a shipyard for smuggled weapons. Tony and Ziva get trapped in a container at a shipyard after seeking refuge from a shootout in the ship yard. While inside, they uncover counterfeit bills being used to bankroll a terrorist operation. Meanwhile back at NCIS headquarters, Abby struggles to locate the two agents when the GPS chips in their cell phones show they are out of range.

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. The team works to piece together the Lt. Commander's location by tracking a distress call she made from her cell phone. Believing her captors have abducted the Lt. Commander to commandeer the nuclear shipment, NCIS must move quickly to find the missing woman and protect the classified location of the weapons.

When the wives of two Marines are murdered, Gibbs and the team are called in to investigate. Gibbs and the team fear the murders are racially motivated. The team works together to find the killer and protect another woman and her newborn baby who they fear are the next targets.

Gibbs and the NCIS team make a disturbing discovery when they bust an illegal automotive chop shop run by Marines. The NCIS team is shocked when they discover the severed head of another Marine in the back of one of the shop's cars. When the Marines running the stolen car ring are ruled out as suspects, the team looks for clues that will lead them to the rest of the Marine's body and the person responsible for the crime.

The team investigates the mysterious explosion of an ambulance that is supposedly carrying the remains of a Marine killed in a car crash. As the team works to confirm the identity of the Marine's remains, they discover the ambulance was rigged to explode and that the DNA of the victim does not match that of the deceased Marine. As Gibbs pushes the team to figure out who the victim is, he discovers that the family of the missing soldier is keeping a secret.

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. When the NCIS team searches the missing Marine's campsite, they quickly determine that the Marine was not alone and they begin to search for his camping partner, a woman who they hope is still alive. As the investigation progresses, the team discovers that a number of past accidents in the park seem to be linked to a possible serial killer who is using the national forest as a location to torture and kill women.

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. In order to establish contact with the bomber and his hostages, Gibbs manages to get into the classroom and leaves Tony to act as lead on the mission. With snipers poised to take the teen down, Gibbs realizes that the 17-year-old might not be acting on his own, and the NCIS team races to find out who may be controlling him from the outside.

Gibbs and the team are called in when a couple of kids stumble upon the body of a missing Marine in a frozen lake. As the NCIS team searches the frozen lakebed for clues, they come across three more bullet-ridden bodies. During the autopsies, Ducky and Gibbs discover that the three additional victims had gang tattoos. With this crucial piece of information, the team works to uncover the Marine's connection with a deadly street gang.

Academy Award and Emmy Award nominee Nina Foch ("Back When We Were Grownups") reprises her role as Ducky's eccentric, elderly mother. Gibbs and the team are called in when a Pentagon cryptographer suspected of spying apparently commits suicide. With their prime suspect dead, the NCIS team must uncover whether or not she was the Pentagon's mole. The team quickly discovers evidence that indicates the young woman was not alone when she died. Now faced with a potential murder, Gibbs and the team follow the clues left behind to find her killer and expose the mole.

Gibbs and the team go into protective overdrive when Abby becomes the prey of a stalker. After discovering that a grisly murder scene was staged, the team realizes that Abby was the intended target when some key evidence contaminates her lab and almost kills her. The NCIS team uncovers some unsavory characters in Abby's past and must work quickly to uncover who is out to get her.

Ziva becomes the focus of an NCIS investigation when a suspect in her custody dies. Ziva is in shock when a routine tactic she uses to subdue a suspect might be the cause of his sudden death. As Ducky and Abby work to clear Ziva's name, Gibbs learns that Director Shepard has been kidnapped by their dead suspect’s brother who is demanding the release of his brother, who he doesn't know is dead, in exchange for the NCIS director.

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. As the team attempts to put their feelings about Gibbs' injury aside and work on the investigation, Tony steps into the role of senior agent, causing a bit of resentment from other team members. Meanwhile, while recovering, Gibbs is flooded with memories of his past that he had long struggled to suppress.

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. As the team tries to track down the terrorists behind the bombing that injured Gibbs, they learn that the terrorist group is planning another bombing of 9-11 magnitude -- and that Gibbs has information about their plan. Meanwhile, Gibbs receives a visit from his former boss and mentor that conjures up suppressed memories. As Gibbs regains his memory, he finds himself on a race against the clock to fill in the gaps and stop the terrorists.