I've already got the Ruby gem stone and I've handed it in but where is..

First, you use cut on the door in the Dotted Hole. It will fall open. Go in then you will see four holes in the ground.

Follow these directions to make it to the sapphire.
Up, left, right, down. If you do it correctly you'll keep on falling onto different floors. If you follow these directions you'll find the sapphire. But then the scientist will come take it.

He'll also tell you the second password to the rocket warehouse. After you beat the last rocket.There's a little passage on the left side of the room. Go in there and you'll find the scientist,battle him and he'll give you the sapphire back. I guess you know what to do next!

Good Luck.

The Sapphire is in Dotted Hole, on Island Six (in Ruin Valley). Decipher the Braille slabs as you go down; they tell you which hole to take. (You can use the series of Braille mounds in Mount Ember or in Ruby or Sapphire's Sealed Chamber, or consult a dictionary.) At the end of the line you will find the Sapphire, but a scientist will snatch it from you. He gives you the second password. You should know what to do from there.