Instructions
Fly to Pacifidlog town. Make sure to bring a Mach Bike, a good number of Ultra Balls or Timer Balls, and a Pokemon capable of using Surf.
Use Surf in the town and go right, towards Route 131.
Halfway through the zone, head north through the break in the rocks. Follow the path to the island named Sky Pillar.
Walk up each level of the tower. Some levels have cracks on the ground. Use the Mach Bike to ride over the cracks, or else you'll fall down to the previous level.
Walk out onto the top layer of the tower, save your game, and engage Rayquaza.