While on Air Force One, a Navy Commander dies under mysterious circumstances, forcing an emergency landing in Wichita. The NCIS Major Case Response Team travels to Wichita to take jurisdiction over the investigation, but are eventually forced into a joint investigation with the FBI and Secret Service. Working with Special Agent Caitlin “Kate” Todd of the Secret Service, the NCIS team is tasked with discovering what happened and why. It’s eventually discovered that a terrorist group is planning to kill the President and one of their members is on the airplane, having been vetted as a reporter. But just before the terrorist can succeed, Gibbs intervernes at the last second and kills the terrorist when he resists arrest. After the investigation concludes, Kate resigns from the Secret Service for good and is offered a job as an NCIS field agent which she accepts.

Recurring characters: Alan Dale as Director Tom Morrow, Joe Spano as FBI Agent Fornell and Pancho Demmings as Gerald Jackson

A Marine dies during a night-time training jump. The culprit seems to be a faulty parachute, but the standard investigation reveals that the death might not have been an accident after all. As the case is upgraded to a murder investigation, Gibbs and Kate quickly find that the case isn’t as straightforward as it first seemed. Meanwhile, Abby is swamped with forensic red herrings, and DiNozzo switches his reserve parachute in an attempt to trick a confession from a suspect.

Recurring characters: Pancho Demmings as Gerald Jackson and Patrick Labyorteaux as LT Bud Roberts

When a Naval Commander is murdered, seemingly during a freelance drugs deal gone sour, the media is quick to link him to drug trafficking and the evidence stacks up. Being a former Marine himself, Gibbs refuses to believe that a good officer could be so corrupt, and in his efforts to clear the Commander’s record and good name, uncovers a turf war between two rival drug gangs, and a terrorist’s scheme to knock out the national power grid. The NCIS team is aided in its investigation by the DEA, and FBI Special Agent Tobias Fornell.

Recurring characters: Alan Dale as Director Tom Morrow, Joe Spano as FBI Agent Fornell and Pancho Demmings as Gerald Jackson

One of Gibbs’s former team members, NCIS Special Agent Stan Burley (Joel Gretsch) who is Agent Afloat on the USS Enterprise calls for assistance when a sailor suffers a meth overdose while on leave, despite having never taken the drug. When another sailor is admitted to sickbay under the same circumstances, Tony and Kate investigate the source of the drugs within the crew while Gibbs begins to suspect that a senior officer on the ship may secretly be doping the crew with performance-enhancing drugs.

Recurring characters: Pancho Demmings as Gerald Jackson

NCIS Norfolk Case Agent Timothy McGee works on a case of a partially dissolved corpse found in a barrel of acid at the Norfolk Naval Base, and calls in the Major Case Response Team to help him. As the investigation continues, it soon becomes apparent that the killer took steps to prevent the body from being identified. Gibbs quickly comes to believe that the motive for the brutal murder was identity theft and his suspicions are further confirmed when it’s revealed that although a submariner is dead, no-one has been reported missing, leading Gibbs to believe that an imposter is on one of the submarines. Tony, Abby, and McGee are tasked with identifying the deceased, while Gibbs and Kate are sent underwater on a submarine to vet five possible suspects, one of whom might have been responsible for the murder and also prevent a biological attack from happening.

Recurring characters: Sean Murray as Timothy McGee and Pancho Demmings as Gerald Jackson

First appearance of: Timothy McGee

The team heads for Cuba when Ducky and Gerald discover that a dead Guantanamo Bay translator they’ve been working on has a stomach full of emeralds. NCIS Special Agent Paula Cassidy proves to be more than a match for Tony when he is ordered to investigate her involvement, while Gibbs and Kate try to discover where the emeralds came from, how they ended up in their translator’s stomach, and prevent the assassination of an important prisoner.

Recurring characters: Jessica Steen as Paula Cassidy and Pancho Demmings as Gerald Jackson

First appearance of: Paula Cassidy

When a dead marine seemingly calls his wife on the day of his funeral, Gibbs, Tony and Kate begin investigating. The case quickly becomes complicated, as the marine’s CO apparently has two physical forms, and Tony somehow manages to meet and interrogate the victim’s wife in a park without even leaving the office. As the investigation continues, the marine turns up embalmed, having been killed two days after his funeral supposedly took place. Gibbs suspects CIA involvement, and is soon tracking a rogue operative in an attempt to rescue the deceased marine’s partner before another murder takes place.

Recurring characters: Alan Dale as Director Morrow and Pancho Demmings as Gerald Jackson

Kate immediately bonds with a woman suffering from amnesia after she wakes up and crawls from her grave following a murder attempt, claiming to remember that a bomb is present on a Navy ship and that people will die unless it’s found. Gibbs and DiNozzo identify the woman whose name is Suzanne McNeil as an explosives fabricator who works for a civilian contractor, charged with manufacturing and testing bomb detection devices for the Navy. When one of the woman’s coworkers turns up dead, the team investigates the second murder. Meanwhile Kate attempts to help McNeil recover from her amnesia and recover her lost memories but the case comes to a deadly close when McNeil, having regained her memories drops a powerful bomb onto the floor of her workplace which kills her and her employer who was also her lover and leaves the NCIS team Kate especially emotionally scarred.

Recurring characters: Pancho Demmings as Gerald Jackson

NCIS is called in to investigate the murder of a naval officer at Little Creek Naval Base following an anonymous tip-off. McGee manages to track the tip-off to Langley, suggesting that the CIA has been spying on the base. Gibbs and Kate follow the tip-off, coming across a witness who leads the team to several possible suspects. At first the murder seems to be tied in with work the officer was involved with, but the team soon begins to suspect a more domestic motive.

Recurring characters: Sean Murray as Timothy McGee and Pancho Demmings as Gerald Jackson

When a marine recruiter is killed, the NCIS team quickly discover that a highly intelligent and skilled sniper was behind the attack. Initially, the team believes the sniper had a grudge against the recruiter, but when a second attack occurs the investigation takes on a wider scope. When Gibbs notices that the sniper left a calling card at each scene, he realizes that the sniper was meeting the recruiters before the shooting took place. Hoping to lure out the killer, Gibbs dons his old Marine uniform and takes over in the recruitment office with Kate, his new “commanding officer”, co-ordinating with DiNozzo and assisted by an FBI team.

Recurring characters: Pancho Demmings as Gerald Jackson

A local county sheriff calls in NCIS upon discovering a murdered lieutenant commander by the roadside, quickly followed by the murder of a civilian contractor two counties over. As the team struggle to find a motive or suspects for either case, another murder occurs; this time a naval aviator. Ducky points out that while the murders appear to follow the same modus operandi and seem to have been carried out by a serial killer, some elements are different, indicating that the murders were not carried out by the same individual. A DNA sample draws suspicion onto the widow of the third victim, but she has an iron-clad alibi, leaving Gibbs with a complex investigation and many loose ends to tie up.

Recurring characters: Pancho Demmings as Gerald Jackson

Fornell and Gibbs clash when it is discovered that a marine colonel absconded from Iraq with two million dollars, and returned to the states under an assumed name. Fornell thinks he stole the money while Gibbs believes he’s innocent. The Colonel contacts Gibbs, and explains that he has discovered a conspiracy to siphon funds out of Iraq for use on black ops. Gibbs is drafted in to aid in bringing down the conspiracy, and meets the Colonel’s partner – a lieutenant who had died in Gibbs’s arms years ago. After being arrested for “pissing off the FBI”, Gibbs and Fornell set out to discover the truth behind the Colonel’s claims in a tense standoff.

Recurring characters: Alan Dale as Director Morrow, Joe Spano as FBI Agent Fornell and Pancho Demmings as Gerald Jackson

Ducky responds to an emergency call when the Israeli Embassy sends a Royal Navy officer to NCIS for autopsy, only to find a gunman (revealed in later episodes to be recurring antagonist Ari Haswari) inside the body bag. As Ducky, Gerald and eventually Kate are held hostage in the autopsy lab, the director coordinates with an FBI strike team to negotiate their release. Meanwhile, Kate hesitates when presented with an opportunity to kill her captor, while Gibbs and Tony take more pro-active measures to get their co-workers out safely, ending with a showdown during which shots are fired, one of which hits Gibbs’s left shoulder, leaving both himself and Gerald who had been shot during the siege injured.

Recurring characters: Alan Dale as Director Morrow, Pancho Demmings as Gerald Jackson, Jessica Steen as Paula Cassidy and Rudolf Martin as Ari Haswari

First appearance of: Ari Haswari

A Navy SEAL convicted of double homicide escapes from Leavenworth, resulting in Kate and McGee being assigned to protect the son and in-laws of the escaped prisoner. During the night, the SEAL breaks into the house to see his son before fleeing, leaving Todd tied to a chair and unarmed, her weapon having been taken by the SEAL. Profiling his behavior, Kate theorizes that he may actually be innocent, and had discovered the identity of the real killer while in jail. Gibbs brings in the presiding defense and prosecution attorneys, one of which is Lt. Commander Faith Coleman to go over the evidence while attempting to arrest the true killer before the fugitive delivers his own brand of justice: revenge.

Recurring characters: Sean Murray as Timothy McGee

Special Agent Chris Pacci is brutally murdered while investigating a cold case, prompting a guilt-ridden Gibbs to step in and take over the case while attempting to find Pacci’s killer. The team follows the trail of millions of dollars, and is led to a woman with ties to the thief. The agents take shifts conducting a stake-out on the woman’s house, until Tony’s caught raiding the mailbox. Forced to improvise, he introduces himself as a resident of the neighbourhood and strikes up a conversation based on what he had heard via surveillance. This gives him a chance to get close to the suspect in order to find out more, as he goes on a successful date with her. Meanwhile, Abby makes a shocking discovery which leaves Tony horrified and vulnerable to an onslaught of merciless taunts and teasing from Kate: the suspect they’ve been trailing, Amanda Reed is in fact Lt. Commander Voss, the Officer who faked his own death in a car accident and who’s responsible for stealing money from the Navy. Things come to a head in a bar where Voss/Reed attempts to kill Tony in front of witnesses but Gibbs gets there just in time and shoots Voss/Reed dead, avenging Pacci’s death.

Recurring characters: Sean Murray as Timothy McGee

The disappearance of a marine draws NCIS in to investigate, and it’s discovered that several marines from the same unit have also vanished under similar circumstances. When skeletal remains of one of the missing men is found chained to a pipe in a small sewer room, Gibbs begins to suspect the unit CO (the only team member not dead or missing) as a serial killer. However, after Tony vanishes, the investigation takes on a more frantic pace and McGee is called in from Norfolk to help as Gibbs and Kate work against the clock to find Tony before it’s too late.

Recurring characters: Sean Murray as Timothy McGee

As Ducky meets his new assistant, Jimmy Palmer, Gibbs takes the case of a marine found impaled on a tree stump. The investigation uncovers the sale of decommissioned military weapons on the black market. Tony goes undercover and meets the buyer, only to stumble into an ATF operation. Working with ATF Special Agent Stone, Gibbs poses as a weapons supplier to complete the deal, and must double cross everyone in order to find the corrupt person at the centre of the investigation, and the one responsible for the marine’s death.

Recurring characters: Sean Murray as Timothy McGee and Brian Dietzen as Jimmy Palmer

First appearance of: Jimmy Palmer

Routine training results in the death of a U.S. Navy SEAL lieutenant just days before he was due to deploy on a classified hostage rescue operation. The death is initially dismissed as an equipment malfunction, but Abby discovers that the link attaching the lieutenant to his rappelling rope was made of a weaker material than factory standard, suggesting sabotage and potentially murder. Pressure is applied by the CIA for the investigation to be wrapped up within 38 hours so the operation can continue or else the entire mission will be scrubbed. As the case goes on, Gibbs discovers that the lieutenant had a secret, and that his wife may hold vital information about his death.

Recurring characters: Sean Murray as Timothy McGee and Brian Dietzen as Jimmy Palmer

As Gibbs’s obsession with tracking down the infiltrator who held Todd and Ducky hostage begins reaching new heights, the team grow more concerned about him. McGee works at identifying him with a modified FBI program, while Todd and Tony go for lunch with Ducky. As Tony leaves in pursuit of his “dream woman” who is actually a terrorist, Kate heads back to the office for a video conference with Paula Cassidy, only to be kidnapped and reunited with her captor, now revealed as a Hamas terrorist who is planning to shoot down Marine One – a transport helicopter carrying President Bush and Ariel Sharon. At first, she refuses to cooperate, but she reluctantly relents when the female terrorist threatens to kill Tony after sleeping with him. As Gibbs grows increasingly agitated, the search for the terrorist is narrowed down by McGee and Abby calculating his exact age, and Ducky concluding that he attended medical school. McGee’s program locates him as a graduate of a Scottish medical school. As the terrorist tries to convince Kate to identify Marine One, McGee finally discovers his name – Ari Haswari. The episode ends with Ari and Gibbs meeting each other in Autopsy and then Gibbs shoots Ari in his left arm in revenge for Ari injuring him and Gerald as well as kidnapping Kate. In season two, he claims he did it to help keep Ari’s cover in al-Qaeda intact.

Recurring characters: Joe Spano as FBI Agent Fornell, Sean Murray as Timothy McGee, Rudolf Martin as Ari Haswari, Jessica Steen as Paula Cassidy and Brian Dietzen as Jimmy Palmer