Instructions
Travel to the Ruins of Alph by walking across Johto or by using a Pokemon that knows "Fly" to instantly transport there.
Enter the upper left chamber. Place Ho-Oh at the front of your party to solve the puzzle in the chamber.
Enter the lower left chamber. Have a water stone in your item bag to solve the puzzle in the chamber. You can now access both the upper and lower left sides of the Ruins of Alph.