The ruins are on Seven Island. You need to go to a cave with a boulder puzzle. You need to put the boulders in the right places so that the ruins can be accessed. When you have the boulders positioned, you will "hear" rumbling on the game and the ruins will be accessible, where you can catch Unowns.
If you are talking about the Dotted Hole on Six Island, then the way to get in is using HM Cut on the door. The Sapphire is inside that cave!
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Go to four island and go in icefall cave find HM7 use it to go up the waterfall go to the ladder beat the rocket talk to lorelei leave and go to six island and go to the ruins the scientist should be gone use Cut on the door to open it.
near the ruins of alphaLedyba can be found in pattern bush in green path in six island.
use cut
Go up to the Dotted Hole door on Six Island and have a Pokemon use Cut the door will open without fail but save after entering
In order to open the warehouse door on Five Island, you will have to collect two passwords in order to open the door. The first one is obtainable from two rocket grunt on Mt. Ember (located near One Island), and a scientist at the bottom of dot hole (located on Six Island).