A suppressed SIG-Sauer P220R in a stainless finish is used by Guyman Purcell (Anthony Heald) to threaten Anna Real (Tania Raymonde) in "Eye for an Eye" (S2E17).
In "Forced Entry" (S2E09), Laura Rowens (Megan Ward) uses a Beretta 85F to shoot a man she thought was going to attack her. In "Conspiracy Theory" (S2E19), Catherine Reynolds (Brigid Brannagh) is seen holding the Beretta on her partner in crime.
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 the Season 2 premiere "See No Evil" (S2E01), kidnapper Kyle Grayson (William Mapother) holds one on his hostage while in a standoff with NCIS agents.
In "Vanished" (S02E03) Marine helicopter pilot Captain Todd Newell (Rob Boltin) carries a M1911A1 while hiding out in the Virginia forest and stalking his brother's murderer. In "Call of Silence" (S2E07), Iwo Jima veteran Ernie Yost (Charles Durning) brings his M1911A1 to NCIS headquarters to turn himself in for possibly murdering a fellow Marine during the battle.
The Glock 17 is another frequently-used handgun in the series. In Season 1's "Enigma", FBI Special Agent Tobias Fornell (Joe Spano) is seen drawing a Glock. In Season 2's "Terminal Leave," Navy Lt. Commander Michaela "Micki" Shields (Mary Page Keller) keeps a Glock in her home.
In "Witness" (S2E14), a Glock 17L was found in the convertible sofa bed used by Petty officer Keith Dylan/Robert J. Thorn. It was misidentified as a SIG-Sauer and can be clearly seen in multiple other scenes as a Glock, most clearly when being test-fired into a bullet capture chamber by Abby Sciuto (Pauley Perrette).
In "Black Water" (S2E11), what appears to be a Kimber Custom TLE II fitted with a scope and laser sight is found in the den of Thomas McAllister's father. It's identified as a "Colt .45". Private investigator Monroe Cooper (Mike Starr) finds the pistol.
In "Pop Life" (S2E16), club owner Ian Alfred "Bulldog" Hitch (Steven Brand) is seen using a Ruger GP100 to threaten one of his dancers, Samantha "Jade" King (Mya Harrison).
In "Terminal Leave" (S2E06), DiNozzo is seen carrying a Smith & Wesson Model 60 as his backup weapon when jogging with a Navy commander. A
Model 60 also appears to be the revolver that Kate conceals in a thigh holster in "Black Water" (S2E11).
In the Season 2 finale "Twilight", several terrorists can be seen firing AKMS rifles at Gibbs and the team to no avail. The weapon is also used by various other characters in the series.
Imperial Japanese soldiers are seen with the Type 99 Arisaka Rifle as Ernie Yost (Charles Durning) remembers his time on Iwo Jima in "Call of Silence" (S2E07).
In Season 2's finale "Twilight" (S2E23), Gibbs (Mark Harmon) uses a police Remington 870 to flush out the terrorists in the warehouse. Kate (Sasha Alexander) uses it during the shootout before running out of ammo and tossing it to take a bullet for Gibbs.
In "Vanished" (S2E03), a Marine AH-1 Cobra (most likely the same civilian-owned modified version seen in Season 8 of JAG) fitted with what is supposed to be a General Dynamics M197 Vulcan is discovered within a crop circle.