In Season 2, FBI Special Agent Fox Mulder (David Duchovny) started carrying a SIG-Sauer P226 as his sidearm. This weapon first appeared in the Season 2 premiere "Little Green Men" (S2E01), when Mulder tried in vain to shoot an alien with his newly-issued P226 (however, despite SIGs' "Hell and Back" reliability, firearms generally do not function when UFOs are around in The X-Files). Following this episode, Mulder would carry the P226 for the entirety of the season. Rarely, some police and government officers would be also be seen with P226s.
Beginning with Season 2, Special Agent Dana Scully (Gillian Anderson) started carrying a SIG-Sauer P228 as her sidearm. Scully is first seen using her P228 in "Blood" (S2E03) and would carry it for the remainder of the season. Mulder and Scully's boss, Assistant Director Walter Skinner (Mitch Pileggi), as well as Agent-turned-antagonist Alex Krycek (Nicholas Lea) are also seen with SIG-Sauer P228s. Other FBI and government agents on the show are also seen using P228s. Mr. 'X' (Steven Williams) also carries a P228 in the episodes "One Breath" (S2E08) and "End Game" (S2E17). In "One Breath", X describes his P228 as a "High-capacity compact SIG-Sauer .40-caliber weapon.". The P228 is only available in 9x19mm, so Mr. X did not correctly describe the weapon's caliber (the prop weapon used in the episode is clearly a P228 and not a P229).
In the episode "Duane Barry" (S2E05), Duane Barry (Steve Railsback) uses a Smith & Wesson 5904 that he took from a guard at the mental institute. He uses the weapon throughout the episode to hold several hostages. The weapon is referred to in the episode as a "Nine-millimeter Smith & Wesson handgun."
Beretta 92FS pistols are seen numerous times throughout Season 2, carried and used by police officers and government agents, as well as military personnel.
In "Little Green Men" (S2E01), Mulder and Scully were chased away from the Arecibo radio telescope site in Puerto Rico by a Blue Beret Crash Retrieval Unit. The Blue Berets were armed with a number of weapons that were considered "futuristic" back in the mid-1990s when the episode was made, including a Steyr AUG, a Calico M955A with a laser sight, and at least two Mossberg 500 Bullpup shotguns. The leader of the team carries what appears to be an airsoft MP5 (see below).
Error creating thumbnail: File missingCalico M955A Intermediate length Select fire carbine - 9x19mmError creating thumbnail: File missingThe Blue Berets firing their assault weapons at Mulder and Scully as they flee the Arecibo radio telescope site in Puerto Rico in "Little Green Men" (S2E01). The Berets are armed with (from left to right) Mossberg 500 Bullpups, a Calico M955A, and a Steyr AUG.
Heckler & Koch MP5A3
What appear to be Heckler & Koch MP5A3s are seen throughout the season. Upon closer inspection, the vast majority are actually Tokyo Marui spring-powered airsoft guns. One of these weapons is notably wielded by the Blue Beret team leader in "Little Green Men" (S2E01). In "Anasazi" (S2E25), a team of black ops soldiers are armed with MP5A3s fitted with the H&K proprietary flash hider (these appear to be the only real, blank-adapted MP5s on the show, instead of airsoft replicas).
What appear to be Heckler & Koch MP5Ks are seen used by government and military personnel, particularly the black ops soldiers in "Anasazi" (S2E25). In reality, these are not real MP5Ks; but rather mock-ups built on the bolt carrier and magazine well of a Kimel AP-9, because the armorers in British Columbia did not have genuine MP5Ks during the 1990s. The same guns have also appeared in Crying Freeman, M.A.N.T.I.S., and The Outer Limits.
The M16A1 was used on a regular basis throughout The X-Files as either a military and/or SWAT weapon. M16A1 rifles can be notably seen in the Season 2 episode "Sleepless" (S2E04).
In the first episode of Season 2, "Little Green Men", Mulder and Scully were chased away from the Arecibo radio telescope site in Puerto Rico by a Blue Beret Crash Retrieval Unit. The Blue Berets were armed with a number of weapons that were considered "futuristic" back in the mid-1990s when the episode was made, including a Steyr AUG, a Calico M955A with a laser sight, and at least two Mossberg 500 Bullpup shotguns. The leader of the team used another airsoft MP5 (see above).
Error creating thumbnail: File missingSteyr AUG (Austrian Army Version) - 5.56x45mmError creating thumbnail: File missingThe Blue Berets firing their assault weapons at Mulder and Scully as they flee the Arecibo radio telescope site in Puerto Rico in "Little Green Men" (S2E01). The Berets are armed with (from left to right) Mossberg 500 Bullpups, a Calico M955A, and a Steyr AUG.
Unknown bolt-action rifle
In "Blood" (S2E03), Edward Funsch (William Sanderson), a man suffering from an extreme-paranoia psychotic break is seen purchasing and later firing on a small carnival with an unknown bolt-action rifle. It is in .308 Winchester (as seen from a box of ammo he uses), has a jeweled Bolt, and scope.
In the first episode of Season 2, "Little Green Men", Mulder and Scully were chased away from the Arecibo radio telescope site in Puerto Rico by a Blue Beret Crash Retrieval Unit. The Blue Berets were armed with a number of weapons that were considered "futuristic" back in the mid-1990s when the episode was made, including a Steyr AUG, a Calico M955A with a laser sight, and at least two Mossberg 500 Bullpup shotguns. The leader of the team used another airsoft MP5 (see above). In addition to this, government agents are seen with Mosberg 500 Bullpups in other episodes.