- "Umm... Did everyone else see that?"
- "You mean a man disintegrate right in front of us?"
- "Really wish I hadn't."
- —Simmons in Cloak and Dagger
The Binary Rifle is a long-ranged sniper-like weapon that is capable of disintegrating enemies on impact. This advanced alien-human hybrid weapon first appears in the episode Cloak and Dagger, being primarily used by the Space Pirates. Upon seeing the weapon's effect, the Blood Gulch Crew become silent and horrified.
- Space Pirates: After Felix and Locus are payed by the two Chorus factions in alien artifacts, they bring the weapons to Control to repair them before the Space Pirates can use them. The Space Pirates use them to kill the inhabitants of F.A.C. Outpost 37 and, when the Blood Gulch Crew interrogate the mercenary Zachary Miller later, another Space Pirate kills Miller using a binary rifle in Accentuate the Interrogative.
- Carolina: In Fed vs. New, Carolina is shown briefly using a binary rifle to disable the radio jammer at Radio Jammer Station 1C, along with the rest of the Blood Gulch Crew, in order to contact the New Republic and Federal Army of Chorus. She then uses it to hold Felix at gunpoint when the latter attempts to kill Tucker.