I was super confused at the point where I saw I had to restart a generator, I ducked down into something and got into an area where I shot some monster , pushed two buttons to start a generator then went back to the surface where I saw something below, but wondered if I missed something on the floor where I hit the two buttons?

This is for Unreal II the awakening.

I can't recall what you're describing. However, I suggest going on Youtube and looking for Unreal II walk through videos.

Or, you can read a walk through here:

http://www.gamespot.com/articles/unreal-ii-the-awakening-walkthrough/1100-2911241/

I believe you'll want to read the walkthrough for the level: Sanctuary