Prototype weapons are rare weapons in The Conduit. They are not carried or dropped by enemies, and can be found only by solving ASE puzzles. These weapons cannot be used in multiplayer, and are modified versions of existing weapons in the game. The one thing they have in common in appearance is that their colors are black and red. There are three of them, which are:
- Deatomizer Mk9: a variant of the Deatomizer Mk4. Its target scope is red, and the rest of the weapon is black. It fires the same shots that the Deatomizer Mk4 would if it were charged. This prototype cannot be charged.
- Striker: a fully-automatic version of the Strike Rifle. Its bio-mass is red, and the rest of the weapon is black.
- The color schemes of the weapons match the Destroyer Armor in Conduit 2, which suggests that the Destroyers manufactured and hid these special weapons.