It's actually pretty easy. You know there are two places where you can raise or lower the level of water in the temple. At the beginning, you just have to lower the water to the minimum level, then check all the areas in that floor. After, you raise the level of water once and check all the areas on the second floor. Don't forget to recheck the areas on the first floor. I know there's an area that you can't access in the main tower of the entrance until you raise the water level once. After that, you raise the level again and check all the areas on the last floor. You then have to recheck the areas that you probably couldn't access in the two floors below before you raised the water level, and rinse repeat if you forgot something or need to get the temple's item (longshot, ah!).
Random game thought :
Why is Bionic Commando Rearmed 2 getting so much hate? We finally get a real game and they're not even satisfied... I'm starting to hate the gaming community so f****** much...
