I tried my best to understand what was going on here, but I'm afraid I failed. After from a few false starts when I kept shooting and didn't realise why I was dying, I then just wandered through the levels until I got stuck in an unfinishable level 3. I wasn't sure what the various sonar noises meant, and I never seemed to need to shoot anything to make my way through the level.
I think I get what you're aiming for, but it would work better if it was a bit more explicit what's happening. It would also be good to have a definite ending to the third level rather than leaving the player stranded and wondering if they've missed something.