One of Priya's bodyguards in Mumbai, India is armed with a Beretta 92A1 in "Wanted". Michael uses one near the end of "Pay-Off" when he goes with Nikita to Dubai in order to start a raid on MDK Industries and save hostages inside the compound.
Beretta 92FS
Ryan uses a Beretta 92FS briefly in "Set-Up" before Birkhoff disarms him. In the same episode, Michael uses it as his main sidearm before Sam disarm him of it in Mumbai. A few Shop agents pursue a wounded Ryan armed with 92FS pistols in the middle of "Bubble".
Beretta 92FS Inox
A Beretta 92FS Inox is shown in a flashback sequence in "Wanted". The fake President Spencer uses a 92FS Inox to shoot her herself in the temple at the beginning of "Set-Up". Nikita uses one in "Canceled" as part of her plan to destroy the Shop permanently.
Beretta Px4 Storm
Wilton Police use the Beretta Px4 Storm in "Wanted" and Nikita takes one after she returning to America from Canada. Michael uses it to threaten FBI Deputy Director Matthew Graham in helping Nikita escape near the end of the same episode. In "Set-Up", it's the main sidearm used by CIA agents operating the Mumbai blacksite with Alex taking it from a CIA agent after disarming him of his sidearm. Ex-terrorist Ramon Esquivel (Simon Kassianides), who now works for the Shop, uses a Beretta Px4 Storm as his main sidearm in "Pay-Off". Ryan takes one from a Shop agent in "Bubble", using it before running out of ammo. Trevor Adrian keeps one in a drawer, which he uses against Nikita in the middle of "Canceled".
The Px4 Storm later becomes Nikita's sidearm in the season.
Beretta Px4 Storm SD
Nikita appears to switch from her standard Px4 Storm to a Px4 Storm SD when she leads a raid on MDK Industries near the end of "Pay-Off", now being her new sidearm. Amanda takes one from a Shop guard and uses it to execute everyone in the control room after she learns of Nikita's raid on the building.
CAA Tactical RONI-G1
MDK Industries security guards in Dubai appear to be armed with CAA Tactical RONI-G1 with possible Glock 17s mounted since they were never fired near the end of "Pay-Off".
Glock 17
Nikita uses the Glock 17 in "Wanted", as do FBI agents in a dream sequence. Virginia State Police officers carry holstered Glock 17s in "Dead or Alive". A CIA agent at the Mumbai blacksite near the end of "Set-Up" uses a Glock, as does a fake Pakistani soldiers planted by the Shop in "Pay-Off". Nikita uses one in the same episode after killing its owner, Another second generation Glock 17 is used by a Shop agent and by a couple of Marines in "Bubble". Colonel Peter Slocum's double (Joshua Peace) uses one in the middle of "Canceled".
Glock 19
A Glock 19 with a mounted suppressor is used by a Shop agent searching Alex's hotel room in Geneva in "Pay-Off".
Smith & Wesson SW1911SC
A Smith & Wesson SW1911SC is used by "the" FBI Deputy Director Matthew Graham (Alex Carter) as his main sidearm in the season.
Zoraki 914
Sonya (Lyndie Greenwood) can be seen with a chrome plated Zoraki 914 in "Set-Up" (S04E03). Alex uses one in Geneva in "Pay-Off".
Zoraki 925
Shop agents use Zoraki 925 in machine pistol configurations as their main sidearm in the season from the 3rd season. Alex takes one to shoot at Priya's bodyguards after she disarms a Shop agent in "Wanted" with one handed to her by Sam in "Dead or Alive", being her sidearm until "Canceled".
Unknown
Revolvers
Chiappa Rhino 20DS
Amanda uses the Chiappa Rhino 20DS with a chrome finish as her main sidearm again in the fourth season.
Chiappa Rhino 50DS
Owen, aka "Sam" (Devon Sawa), uses a Chiappa Rhino 50DS at his main sidearm in the season, which first appeared near the end of "Wanted" when he confronts Alex alone in Mumbai, India. An armed gunman in Mumbai, India has one before Sam disarms him and shoots him in the stomach in "Set-Up". Michael later disarms him of the revolver and uses it against him in the same episode.
Submachine Guns
Heckler & Koch MP5A3
FBI Agents in close protection duties in "Dead or Alive" are armed with Heckler & Koch MP5A3s outfitted with railed handguards. A Pakistani soldier assigned to protect the truck transport a ballistic missile is armed with the MP5A3 in "Pay-Off". Ryan uses the same weapon when he storms MDK Industries in Dubai in the same episode.
Heckler & Koch MP7A1
CIA SOG operators uses Heckler & Koch MP7A1s, first seen near the end of "Dead or Alive" when they capture Alex in her hotel suite.
Heckler & Koch MP5K
Michael uses a Heckler & Koch MP5K in "Pay-Off" when he and Nikita disembark from their plane in Pakistan in order to intercept a ballistic missile truck hijacked by a team sent by the Shop.
IMI Uzi
Priya's bodyguards in Mumbai, India use IMI Uzis, first seen in "Wanted".
Assault Rifles
Colt M4A1
Virginia State Police officers guarding the Graham residence in "Dead or Alive" are armed with Colt M4A1s outfitted with railed handguards and vertical foregrips. US Marines surrounding the Adrian estate in "Canceled" are armed with M4A1s.
Norinco Type 56
At the end of "Canceled", Michael and Nikita witness a guerrilla fighter handing a Norinco Type 56 to a young boy.
SIG SG 552
Ramon uses a SIG SG 552 with an attached dot sight via picatinny railing as his main weapon while he oversees the hijacking of a Pakistani ballistic missile in "Pay-Off".
Zastava M70AB2
A few of Priya's bodyguards in Mumbai, India uses Zastava M70AB2s, first seen in "Wanted" after a human smuggling exchange goes bad.
Zastava M70 (Unknown Variant)
Shotguns
Benelli Nova
Alex hands Nikita her old Benelli Nova Tactical from Season 2 at the end of "Bubble".
Remington 870
FBI agents in a dream sequence are armed with Remington 870s at the beginning of "Wanted".
Sniper Rifles
Barrett M82A1M
A US Marine Corp sniper team in "Canceled" is armed with a Barrett M82A1M when they conduct recon at the Adrian estate Nikita and Alex had seized in the middle of "Canceled".
Heckler & Koch G3SG/1 (modified as a PSG-1)
Nikita uses a Heckler & Koch G3SG/1 visually modified to resemble a Heckler & Koch PSG-1 in the middle of "Dead or Alive" where she and Michael conduct a false flag operation to discredit the fake FBI Deputy Director.
Machine Guns
Browning M2HB
A Browning M2HB is seen mounted on a US Marine Corp Humvee with an armored shield placed to protect the gunner at the start of "Bubble".
Rheinmetall MG3
Pakistani troops guards a Pakistani Army base in "Pay-Off" are seen manning a machine gun nest armed with a Rhienmetall MG3 GPMG. This is correct since the Pakistani Army is armed with the MG3 officially made under license by Pakistan Ordnance Factories.
Rocket Launchers
Norinco Type 69
A Pakistani gunman in "Pay-Off" is seen armed with a Norinco Type 69.