Travel to the southern area of Island 6 until you reach Ruin Valley. You will find a locked door with pillars on either side, each with the word "Cut" written in Braille.
Face the door and use the "Cut" ability on the door to open it.
Go inside the chamber and drop down the hole. This will lead you to a puzzle where you must drop down particular holes in order to advance through the cave.
Drop down the holes in this order: north, west, east, south. This will lead you to the room that contains the Sapphire Gem.
Take the Sapphire Gem to launch the in-game event. A Scientist will steal the Sapphire Gem from you, and will give you the second password you need to enter the Rocket Warehouse.
Exit the cave and return to the Rocket Warehouse on Island 5. You will now be able to enter both passwords to open the way into the building.