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, on the third season premiere of NCIS. 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 short-lived 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, on NCIS. 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.

When the bodies of two assassins are delivered to NCIS from overseas, Tony and Ziva assume their identities undercover and engage in a sexy rendezvous at a luxury hotel in order to find their target.

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.

While searching a Senegalese ship that they believe is being used to smuggle small arms, Tony and Ziva are captured and locked in a container while the team tries to discover their whereabouts.

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. While investigating, 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.

When NCIS busts an automobile chop shop run by Navy enlisted men, then discover a cooler containing a human head in the trunk of one of the stolen cars. The investigation is hampered by a secretive corporation that has swathed itself in layers of insular legal obfuscation.

Two civilian EMT's are transporting a Marine who died in a car crash but their vehicle erupts in flames when they start driving. The Marine's girlfriend who was in the car with him is still unconscious in the hospital. In the hospital Gibbs and the team meet the Marine's best friend, who may know what really happened.

A Park Ranger is taking a group of Boyscouts around Shenendoah National Park, when they stumble upon bear droppings. One of the Scouts pokes around in it, to discover what the bear ate. Instead, he finds dog tags. A search for the remains of a dead Petty Officer ensues.

Somehow the NCIS team is called to the scene of a High School where a teenager with a bomb is holding some kids hostage. One of the kids is in need of her inhaler for her asthma, and another student stands up for her. When she goes to the lockers to get it, she's able to tell Gibbs what's going on inside.

A Marine is found dead under the ice of a small pond. He was involved with helping kids get out of street gangs and join the Marines. The team gets to work on finding out who was the killer.

A member of a Department of Defense Crypto unit is found dead, when she was supposed to go in and get interviewed by Gibbs. Gibbs was investigating the unit on suspicion of information leaks to a foreign country. The dead female's roommate and their commander seem shaken up when they learn of her death. Gibbs and the team investigate.

An older couple is checking into off-base Navy lodging, but when they enter they are shocked to find a gruesome scene. The clerk is immediately under suspicion. We'll also meet Abby's former boyfriend, who's also a goth and runs a crime scene cleanup company.

Tony and Ziva are coming into NCIS headquarters with $5 million and a drugdealer suspect, who dies in the elevator ride up. His brother wants his cash and brother back, but doesn't know he died. When NCIS is not giving in to his demands, he takes extreme measures.

The NCIS is distressed when Gibbs is injured in a terrorist explosion while on assignment. 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. 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.