Michael carries the Beretta 92FS as his sidearm in the 2nd season. Some of Dr. Mars's gunmen in "Falling Ash" carry the 92FS. Division operatives in "Game Change" use the Beretta. A Division Guardian named Patrick Miller uses one in "Guardian". MI6 agents operating in Russia are armed with the 92FS in "Arising". Robby uses one while disguised as a civilian contractor in infiltrating Maxwell AFB in "Crossbow".
Beretta 92FS Inox
Sean is armed with this in Clawback and Fair Trade, serving as his main sidearm throughout the season. Alex uses this to kill a corrupt ICE agent in Russia in the same episode. Michael has this for a sidearm in Origins. An Inox is found in Doublecross.
Beretta Px4 Storm
In Partners, former Division agent Kelly (Katheryn Winnick) is seen using a PX4 during a confrontation with Alex and Nikita.
Beretta Px4 Storm Compact
Ari Tasarov (Peter Outerbridge) is seen removing a Px4 Storm Compact from Sergei Semak's (Peter J. Lucas) desk. A few moments later, Sergei is seen using it to execute a GOGOL official after questioning him. Alex (Lyndsy Fonseca) carries one throughout "Origins" after taking it from a GOGOL operative and uses it in the ensuing gun battle. It becomes her main sidearm for the rest of the season.
Beretta 93R
Michael's (Shane West) sidearm for the rest of Season 2 is a Beretta 93R with the foregrip removed.
Nikita uses a Glock 17 in "Game Change" (S2E1) after disarming a mobster. The fake Belarusian president in "Looking Glass" (S2E5) uses a Glock 17 to threaten Alex. In "Guardians" (S2E10), Zürich police officers carry the Glock while arresting a Division Guardian named Patrick Miller and Nikita in Switzerland. In "Rogue" (S2E14), a detective uses one as his sidearm. Dinah uses one in "Power" (S2E18) to execute a DARPA scientist. US Army MPs carry the Glock 17 in "Wrath" (S2E19). Ian Damascus, his bodyguards, and Suffolk Country police officers all carry the Glock 17 in "Shadow Walker" (S2E20). Nikita uses a silenced Glock 17 in "Crossbow". Division personnel mandated for combat/guard duty are armed with Glock 17s as their main sidearm.
Glock 26
In "Falling Ash" (S2E2), a brainwashed ice cream vendor uses a Glock 26 to assassinate a Senator. Alex carries a Glock 26 with and without a suppressor when she goes to Russia in "Guardians" (S2E10) and "Pale Fire" (S2E11). During Nikita's flashback to her drug-addict past in "Rogue" (S2E14), she used a Glock 26 to execute a plainclothes policeman. Birkoff finds a Glock 26 with an extended barrel during the police station battle in "Shadow Walker" (S2E20) and uses it to kill a Division agent.
Ruger KP89
Alex carries a Ruger KP89 in "Doublecross" (S2E16).
A two-tone P226 is used by Percy in Knightfall to cripple Ramon in order to force him to work for Division.
SIG-Sauer P239
A silenced P239 with a stainless body is seen in "Power".
Walther P22
A brainwashed woman in Falling Ash uses a Walther P22 when she was brainwashed to assassinate a Senator.
Walther P99AS
Nikita uses the Walther P99AS as her sidearm in Season 2, carrying it throughout the season
Zoraki 914
On several occasions, Zoraki 914 blank firing pistols are used. These pistols are capable of semi automatic and full automatic fire, and are used to substitute for conventional pistols and machine pistols.
Smith & Wesson SW1911SC
Michael carries a Smith & Wesson SW1911SC with a stainless slide, blued frame, and wood grips in "Shadow Walker" (S2E20). He is also seen with it in "Dead Drop" (S2E21). This is presumably his new weapon of choice.
Revolvers
Chiappa Rhino 20DS
In "Power" (S02E18) Ari Tasarov (Peter Outerbridge) can be with a chrome plated Chiappa Rhino 20DS (2" barreled version) revolver with a fibre optic front sight.
Colt Python
Kelly uses a Colt Python with a 2.5" barrel taken from a Turkish Gendarmerie officer she killed in Partners. Dr. Henderson appears to be armed with the same weapon in Crossbow.
Nikita carries the MP7 as her primary heavy weapon in Season 2, first seen in "343 Walnut Lane" (S2E6). A MP7 is seen on a table in "Clawback" (S2E7). Nikita and Michael use them again in "London Calling" (S2E8). Nikita is seen with the MP7 in "Shadow Walker" (S2E20) while posing as bank robber. Alex and Sean use MP7s in taking on a two-man Division team in "Crossbow".
Heckler & Koch MP5A3
Division agents are armed with a tactical foregrip in Clawback. CO19 officers in London Calling are armed with the MP5A3 with a tactical foregrip with a flashlight attached. A Division commando team in Dead Drop are armed with the same MP5A3s from Clawback.
Heckler & Koch MP5K
An MP5K is seen in "London Calling" in the hands of a Tupolev henchman. Michael uses one in Switzerland in "Guardian". In "Sanctuary", rogue Guardians seize control of an Oversight-owned mansion in rural New Jersey. Percy uses the MP5K in "Rogue". Carla takes one in "Doublecross" after being wounded by Birkhoff. Some of the bodyguards of Ian Damascus in "Shadow Walker" are armed with this. A two-man Division team faces Alex and Sean in "Crossbow".
TDI Vector
Birkhoff (Aaron Stanford) carries a TDI Vector after Sean breaches the safehouse in "Sanctuary" (S2E12). Roan (Rob Stewart) and Patrick carry them during the warehouse battle in "Rogue" (S2E14) and "Doublecross" (S02E016).
IMI Uzi
Michael uses an Uzi in Game Change. Oversight sentries carry one in Sanctuary as well.
IMI Mini-Uzi
Nikita dual-wields a Mini-Uzi along with her MP7 in "343 Walnut Lane" after Micheal is hit. Another Mini-UZi is seen on a long table in "Clawback".
Calico M950
A brainwashed Alice (Julie McNiven) in Falling Ash is armed with a Calico M950 outfitted with a scope when Dr. Mars plays a music file when Owen instructs him to download files for the Regiment.
Rifles
AKM
In "Guardians" (S2E10), GOGOL agents deployed to Switzerland are armed with AKMs with Picatinny railings and modern furniture. Nikita and Owen use them, taken from dead GOGOL agents. GOGOL agents carry the AKMs again during the gunbattle in "Clean Sweep" (S2E13). The customized AKM seemed to have been modeled on the King Arms AK-74 Tapco airsoft gun, and it is possible some of the rifles seen in the background are in fact airsoft guns.
Zastava M70
Tupolev henchmen were armed with the M70 in "London Calling". In "Guardian", GOGOL agents on patrol around the perimeter of the Semak Estate in Russia are armed with the M70AB2s.
AKMS
Armenian Border Guards are armed with the AKMS in Partners. Roan, pretending to be a GOGOL agent, uses one in "Doublecross".
Beretta ARX-160
Nikita uses a Beretta ARX-160 in "Rogue" (S02E14), fighting alongside Michael in the warehouse to save Carla. This is the first appearance of the ARX-160 in a television show. Micheal carries the ARX-160 during the steel mill shootout in "Doublecross" (S2E16).
Colt Law Enforcement Carbine
One of the Division agents in "343 Walnut Lane" carry Colt Law Enforcement Carbines fitted with a telescopic sight. The weapon has also been modified with a number of Magpul accessories, including PMAG with ranger baseplate, a UBR stock and an MOE handguard. The weapon is later picked up and used by Roan (Rob Stewart).
IMI Tavor TAR-21
In Falling Ash, Owen uses the Tavor TAR-21 as his main weapon when he and Michael raid Dr. Mar's fake therapy clinic. A few Division operatives uses this in "343 Walnut Lane".
Colt M16A1
Michael (Shane West) uses a Colt M16A1 fitted with an M203 (along with the correct leaf and quadrant sights) in "343 Walnut Lane" (S02E06).
Colt M16A2
US Marines are armed with Colt M16A2s in "Homecoming".
Custom AR-15
Sean Pierce (Dillon Casey) carries a custom AR-15 in "Sanctuary" (S2E12) and "Clean Sweep" (S02E13). Nikita uses it again in "Dead Drop" (S2E21). It appears to be the same weapon Micheal used in Season 1.
M4A1
Division operatives sent to kill Nikita and Michael are armed with M4A1s with C-More red dot sights. In a flashback, Roan (Rob Stewart) and a team of Division agents use the rifle while disguised as American soldiers. Michael also uses an M4A1 with Magpul MOE furniture with a C-More Tactical RDS in "Clean Sweep" and a telescopic sight later.
SIG SG 552
The SIG SG 552 appears to be the stand-issue Division assault rifle and are used by Division personnel with, and without the suppressor and C-MORE sight. In Knightfall, a flashback shows Division guards standing guard behind Ramon with 552s. A uniformed Belorussian Presidential Security Service officer uses one in Looking Glass. Division tactical teams are armed with the SG 552 during a raid in Berlin, Germany in Dead Drop.
Shotguns
Benelli Nova
Alex (Lyndsy Fonseca) carries a short-barreled Benelli Nova Tactical version with a dot sight and collapsible stock in "Wrath" (S2E19) and " "Shadow Walker" (S2E20)
Serbu Super Shorty Remington 870 Shotgun
Michael is armed with a Serbu Super Shorty with a foregrip in "Rogue" and "Homecoming".
Valtro PM5
GOGOL operatives carry Valtro PM5 pump-action shotguns with detachable magazines during the forest shootout in Turkey at the end of "Partners" (S2E4).
Sniper Rifles
Ruger 22 Charger
Alex uses a custom Ruger 22 Charger with an extendable buttstock, scope and suppressor in Knightfall.
A Browning M2HB can be partially seen in "Homecoming".
Heckler & Koch HK21
An HK21 machine gun is seen in Nikita's safehouse in "Dead Drop" (S2E21)
M249 Paratrooper SAW
An M249 Paratrooper SAW is seen in Nikita's safehouse in "Doublecross" (S2E16). Birkoff briefly picks it up and loads an M16 magazine into the SAW in "Dead Drop" (S2E21)
Grenades
M67
A M67 is used by Michael to intimidate Division personnel in "Homecoming".
Division Agent Wyatt (Andrew Hinkson) uses a FIM-43 Redeye surface to air missile launcher in "Doublecross" (S2E16), where it is incorrectly depicted as an unguided rocket launcher.
RPG-NH-75
An RPG-NH-75 is used in Switzerland to take out a Swiss police van to retrieve the black box.
Others
Automated Machine Gun
In Partners, an automated machine gun based from an M4-type rifle with a 100-round magazine was used near the Turkey-Armenia border to "shoot" at Nikita.
Cane weapon
Alex was armed with a cane that was actually a firearm in Falling Ash. It was never used since she intervened to save a Senator from being assassinated.
Molotov Cocktail
Used by a Tupolev henchman in "London Calling" to kill Michael hiding in the shed.