Swim in the circled area to find a tunnel system. Swim through that and their should be an opening on the right.
This is at the very start. The circle shows the button which opens the tombstone. This is both a secret area and easter egg (translator message at picture.)
The arrow on the left leads to a hole in the roof, and the arrow on the right will lead you to the picture below.
Very cool nali hide-out.
Go to the room right after you cross the bridge and turn around. Fire at the button in the red box that I've drawn then look to your right as a part of the wall opens. Run in, grab the jumpboots and proceed to the picture below.
There ya go! Follow the red arrows using two jumps and save the last one at the end ensuring at safe drop after you get the super health!
An area that was supposed to be opened by a nali but I guess was cut-out or forgotten? Use the 'ghost' command to get to it. You can also do 'admin causeevent secretnalio' and it opens a little bit then closes.