In Operation Break Down, Breakdown gets taken out in a single shot. People have since asked why they didn't use that gun again when he and Bulkhead break out. Having seen the episode again I can see they did. The energy cannon the helicopter had was firing the things. You can see a similar trail when Breakdown is first hit. Also when they are being fired at you can see the tip of the beam has something that looks very much like the disk that took him down. So there you go. They were using it.