Trinity (Carrie-Anne Moss) carries a pair of Beretta 92FS Compact pistols as her sidearms in this film and The Matrix Revolutions (although she is only seen using one in this film). She pulls one of her Berettas on Persephone (Monica Bellucci) when she desires to kiss Neo (Keanu Reeves). She later pulls one of them and fires it into one Twin's arm when he blocks open a door leading to a parking garage.
IMI Desert Eagle Mark XIX
As per the norm in The Matrix Trilogy, the Agents in the film can be seen wielding IMI Desert Eagle Mark XIX pistols in .50 AE. Smith (Hugo Weaving) uses them to terrifying effect when a group of his clones, all carrying identical Desert Eagles, volley fire them at Neo, Morpheus, and the Keymaker (Randall Duk Kim). Unlike the first film, the Desert Eagles in this film have a polished finish instead of the original Matte black.
Glock 18C
Morpheus (Laurence Fishburne) uses a Glock 18C in the confrontation with the Twins in the parking garage, then in the following freeway chase scene, where he uses it to destroy the Twins' Cadillac Escalade after using a katana to help flip the vehicle. Morpheus's Glock 18C is initially loaded with a 19-round magazine during the scene in the parking garage, then reloaded with a 33-round extended magazine during the freeway chase.
COP 357 Derringer
After agreeing to help the protagonists, Persephone (Monica Bellucci) kills one of her husband's henchmen and threatens another with a COP 357 Derringer with pearl grips, loaded with silver bullets.
SIG-Sauer P229 Sport
Ghost (Anthony Brandon Wong) packs a stainless steel SIG-Sauer P229 Sport as his sidearm. He is briefly seen loading it just before the car he and Niobe (Jada Pinkett Smith) are riding in is rear-ended by a semi truck whose driver has changed into an Agent.
Walther P99
While making their way through the hallway of doors, the protagonists have an unexpected encounter with Agent Smith (Hugo Weaving). When Smith tells them that he "wants everything", Morpheus pulls out a Walther P99 and holds it to his head, asking if "everything" included a bullet from the gun. Before Morpheus can fire, a swarm of Smith clones burst in and overpower them. Bane (Ian Bliss) briefly tries to draw a Walther P99 on Agent Smith before being coded over by him.
Shotguns
Stevens 67 (Sawed-off)
During the meeting where the machines' plan to attack Zion is revealed, one of the Zion rebels guarding the door is seen carrying a nickel Stevens 67 shotgun with a sawed-off barrel, black pistol grip and foregrip.
Smith & Wesson 3000 Shotgun
During the meeting where the machines' plan to attack Zion is revealed, one of the Zion rebels stands guard with what appears to be a Smith & Wesson 3000 shotgun.
Submachine Guns
Heckler & Koch UMP-45
During the freeway chase, one of the Twins (Adrian Rayment and Neil Rayment) opens fire on the protagonists with a Heckler & Koch UMP-45 fitted with a C-More red dot sight and an almost bottomless magazine. Showing no concern for innocents caught in the crossfire, he opens fire on a luckless Chevy Tahoe SUV that winds up between him and his target, causing it to flip and trigger a spectacular chain-reaction pileup.
IMI Micro Uzi
Trinity (Carrie-Anne Moss) opens the film by diving out of a high-rise office building's window while wielding two IMI Micro Uzis, firing them at a pursuing Agent. It begs the question where she kept them though, as she is wearing an almost skintight outfit and no evidence of any carried weapons after being thrown about by an Agent just prior.
Calico M951
During the meeting where the machines' plan to attack Zion is revealed, one of the Zion rebels stands guard with a Calico M951 submachine gun.
The Museum Fight
When Neo is confronted by the Merovingian (Lambert Wilson) and his henchmen in the museum, the thugs are seen opening fire on Neo with several rifles and submachine guns, including the following:
IMI Uzi
One of The Merovingian's henchmen fires an IMI Uzi at Neo (Keanu Reeves), but Neo stops the rounds in mid-air.
M1928 Thompson
One of The Merovingian's henchmen fires an M1928 Thompson at Neo (Keanu Reeves), but Neo stops the rounds in mid-air.
Colt RO635 9mm SMG
One of The Merovingian's henchmen fires a Colt RO935 9mm SMG at Neo (Keanu Reeves), but Neo stops the rounds in mid-air.