The Rogue Prion Gun is a weapon designed around the principles of the Mad Cow Disease. It fires a projectile that will drive an enemy into a frenzy when it hits the laser. Someone that is affected by the Prion Gun's laser projectile will either sit around doing nothing, occasionally shoot the player, or attack it's friends. It's NETRICSA description states that it will make the target explode 20 seconds after they're hit by the laser, but this never happens.
The Rogue Prion Gun is not very effective. The confuse effect doesn't make the enemy target other enemies often, if at all. The player is much better off using another weapon and killing an enemy with it instead of using the Rogue Prion gun and hope that the enemy will stop shooting them.
The Rogue Prion Gun can be useful for temporarily “stunning” a powerful enemy, such as a Gunrilla, so that the player can focus on other targets. A confused enemy will usually just stand around, giving the player some breathing room to target other enemies. Then, when they've finished off everyone else, they can kill the enemy that was hit by the Rogue Prion Gun.