The original idea was to win by wasting all of your bullets, but receive some sort of "okay" score if you only shot the "bad" guys. We strayed from that and some miscommunication led to the ending message being what it is. I can't fully answer your question on the logic behind it due to poor planning haha.
Definitely going to participate in more trijams! I think these will also help how I approach 48/72 hour game jams too