Shaders and my Models DON'T MIX

So when working with the shader it looked nice with how it shows things the way we wanted it to be, but somebody in the group wasn't fully satisfied with it. He wanted the shader have it to where you could somewhat see stuff but when you use the sonar it would show it fully. So when the shader changed to do this new kind of effect, it didn't exactly go well with my models. Since the way that it was working was with it messing with opacity you could see through the model. And since opacity was what we changed, if you look at the models in a certain way, you couldn't see parts of it or just looked wrong. So with so much fiddling with it and trying to make it look right, I ended up changing all the important models like the enemies back to the old way where they looked a lot nicer.