Customized Remington 870s are seen wielded by several FBI agents conducting an entry and arrest near the beginning of "Grotesque" (S3E14). The shotguns feature short barrels and forends with Butler Creek tactical synthetic loop pump-grips, forend mounted weaponslights, pistol grips with full buttstocks, as well as heatshields over the barrels and door-breaching muzzle brakes. Though some of these features are not clearly seen, they match those of custom Remington 870s that have appeared in the films Timecop, Crying Freeman, and several other movies and TV shows filmed in British Columbia. One of these shotguns also previously appeared in the first season, lacking the weaponlight and full stock.
A custom Ithaca 37 "Stakeout" with a chrome finish on the barrel and magazine tube and an MP5K-style pump-grip is briefly glimpsed in the hands of FBI agents in "Grotesque" (S3E14) and "Pusher" (S3E17). This gun can also be seen in several episodes of the television series Supernatural, Human Target, Painkiller Jane, and several other TV shows filmed in British Columbia.
What appears to be a USAS-12 Shotgun is seen wielded by one of the black ops soldiers guarding what appears to be a recovered UFO in "Nisei" (S3E09).
Error creating thumbnail: File missingDaewoo USAS-12 CQ with 20-round drum - 12 Gauge. Notice that unlike the original USAS-12, the CQ version lacks the front sight, and also has a re-designed carry handle. This version is typically seen in productions filmed in British Columbia, Canada (i.e. Stargate SG-1, Jumanji).Error creating thumbnail: File missingIn the center is what appears to be a USAS-12 in the hands of a black ops soldier in "Nisei" (S3E09).Error creating thumbnail: File missingThe soldier conducting a roving patrol in the background on the left has what appears to be a USAS-12, A CQ variant given what appears to be the lack of a front sight. The soldier in front of him has a Ruger MP9.
Trivia
In "War of the Coprophages" (S3E12), Scully is seen clearing her S&W 5906. A rarity in most films and TV shows, this is the first time in the series such an action is performed on-screen by one of the main actors.
Error creating thumbnail: File missingScully (Gillian Anderson) is seen here in "War of the Coprophages" (S3E12) cleaning her Smith & Wesson 5906 while speaking to Mulder. This is the first time of of the main actors is seen doing this in the show. Note again the blued hammer and trigger of Scully's particular 5906.Error creating thumbnail: File missingScully cleans the barrel of the 5906.Error creating thumbnail: File missingScully chats with Mulder while cleaning her gun. Note the remaining components (slide and frame) on the table in front of her, along with the magazine, ammunition, and holster toward the left.