The SIG-Sauer P228 is the main sidearm of nearly all the NCIS agents in the series including Special Agents Leroy Jethro Gibbs (Mark Harmon), Anthony DiNozzo (Michael Weatherly), and Timothy McGee (Sean Murray). Mossad Officer Ziva David (Cote de Pablo) and Director Jenny Shepard (Lauren Holly) also carry the SIG.
Beretta 92FS
The Beretta 92FS (used in lieu of the Beretta M9) appears as the issued sidearm of various military personnel and in the hands of various characters throughout the series. In Season 3's premiere "Kill Ari, Part 1" (S3E01), terrorist Ari Haswari (Rudolf Martin) holds Dr. Mallard's assistant, Gerald, hostage with one. Gibbs also keeps one in his car during the events of "Kill Ari, Part 2" (S3E02), as it is seen while he and Jenny are staking out Ari's safe house. Port Security Chief Matthew Lake (Daniel Roebuck) pulls a Beretta in "Boxed In" (S3E12).
Beretta 85F
The North Korean sleeper agent Yoon Dawson (Esther Chae) holds a suppressed Beretta 85F in "Light Sleeper" (S3E14).
Beretta Cougar
In "Light Sleeper" (S3E14), a .40 caliber Beretta 8040 Cougar F owned by Marine Sgt. Malcolm Porter (Tim Griffin) is identified as the murder weapon in the shooting of two military wives. While examining it in her laboratory, Abby embarks on a brief segue on a critics' description of the .40 S&W round as a "Short and Wimpy," when measured against the 10mm Autoload. The handgun appears to be Inox variant.
A Walther PPK/S is held by Dr. Elaine Burns (Barbara Niven) in "Silver War" (S3E04).
Walther P99
A kidnapper is seen about to use a suppressed Walther P99 on a kidnapped Marine right before Gibbs and the team breach the room in "Honor Code" (S3E07).
Revolvers
Colt 1860 Army
In "Silver War" (S3E04), a coffin is unearthed containing several weapons from the Civil War, including a Colt 1860 Army revolver.
LeMat 1861
In "Silver War" (S3E04), a coffin is unearthed containing several weapons from the Civil War, including a LeMat 1861 revolver.
Smith & Wesson Model 19
In "Deception" (S3E13), a security guard holds a Smith & Wesson Model 19 on Ziva and Tony, but Ziva kicks the weapon out of his hands.
Smith & Wesson Model 37
Gibbs (Mark Harmon) carries a Model 37 with a black finish in an ankle holster as his backup weapon. In "Mind Games", he uses it to threaten sadistic serial killer Kyle Boone (Christopher Shyer). In "Probie," he gives it to McGee, whose weapon has been temporarily confiscated, to back Gibbs up as they go to question a suspect.
Submachine Guns
Heckler & Koch MP5A2
SRT members are also seen carrying Heckler & Koch MP5A2's during the hostage situation at the school in "Bait" (S3E18).
Intratec TEC-9
An Intratec TEC-9 is seen in Abby's lab in "Iced" (S3E19).
Rifles
Enfield Pattern 1853
The Enfield Pattern 1853 rifle is carried by Union re-enactors in "Silver War" (S3E04).
Henry 1860
In "Silver War" (S3E04), a Henry 1860 is seen used by a Civil War reenactor.
In "Ravenous" (S3E17), a scoped Ruger Mini-14 is carried by Park Ranger James Landis (Todd Allen). Gibbs also used the Mini-14 to shoot Park Ranger James Landis in the butt.
Spencer 1860 Saddle Ring Carbine
The Spencer 1860 Carbine is one of the Civil War-era weapons unearthed in "Silver War" (S3E04).
The Blaser 93 sniper rifle is one of the sniper rifles Abby tests in her lab in "Kill Ari, Part I".
Bravo 51
The Bravo 51 is featured prominently in the first 2 episodes of Season 3. Gibbs says the rifle is referred as a 'Kate', as it was first used by Ari Haswari (Rudolf Martin) in the Season 2 finale "Twilight". In Season 3's premiere episodes, "Kill Ari, Parts I and II", Ari is seen handling one again. In Part I, it's also one of the weapons Abby Sciuto (Pauley Perrette) test-fires in her lab as well as handled by Gibbs. In Part II, a suspect is seen fleeing from Gibbs and Jenny after opening fire on them.
An M40A1 sniper rifle appears in "Kill Ari Part I" and "Kill Ari Part II" as one of the weapons tested by Abby to see if it was used in a murder. The M40A1 was the rifle used by Gibbs in his Marine days and he now keeps it in a case in his basement. Ari is seen holding the rifle in "Kill Ari Part II".
M40A3 Sniper Rifle
A Marine Corps M40A3 sniper rifle is another rifle Abby Sciuto (Pauley Perrette) test-fires in her lab in "Kill Ari, Part I" (S3E01).
Remington 700PSS
A Remington 700PSS is another rifle seen in the lab of Abby Sciuto (Pauley Perrette) in "Kill Ari, Part I" (S4E01). In "Bait" (S3E18), an SRT sniper is seen with the Remington 700PSS rifle.
Remington 700 (Choate Ultimate Sniper Stock)
A Remington 700 bolt action sniper rifle fitted in the Choate Ultimate Sniper Stock is another rifle Abby Sciuto (Pauley Perrette) test-fires in her lab in "Kill Ari, Part I" (S3E01).
Shotguns
Mossberg 590 Cruiser
A Mossberg 590 Cruiser is grabbed by a kidnapper in "Honor Code" (S3E07).