So I found the first and second key no problem. Idk where to find the third one.

Third key only really matters in the Unify route, it's in the grave at the top of the map with dead grass coming out of it.

I might go back and give the Divide route its own special use for the second key, but as it stands the keys only matter in Unify.

Just out of curiosity, is the third key used for something? I found it but I honestly don't remember using it at all at the end of the game unless it's purpose flew over my head or something.