Talk to Celio on One Island, then head to the mountain and talk to the Rockets, they'll battle you and tell you the first half of the password then.

Then head to Six Island and take the lower of the two staircases and move on to the door. The posts on either side have a message in Braille. It says 'Cut,' so just use
Cut while facing the door and it will open.

Fall down the hole. This particular puzzle is maddening without directions.
You must fall down the one correct hole out of four several times, or be sent
back to the beginning. So here's how to proceed: first take the north hole,
then west, then east, then south. Oh, look the Sapphire! Oh wait, never mind...
Well, you now know the second password for the secret Rocket base.
Go up the ladder and exit. Either walk or Fly back to the Pokemon Center.

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