It's how much you use the targetting computer. Don't use it, and you will get a perfect score. Use it and don't fire, and you will lose score. Levels that require 100% efficiency for the gold medal require you to go through the whole level without the targetting computer.
Personally, I only really use it in levels that I have a hard time seeing, such as the second level. (It's been so long since I have seen my copy... I have forgotten the names...)