Go to Pacifldog Town. Then, surf to the east to Route 131 until you pass the boy and girl facing each other, that are separate. You will see an opening between some rocks. Go there and surf west. Keep going and you will see a cave opening. Go through it and enter the building. Go to the top of the building to find Rayquaza. Note: On the second and fourth floors, to pass the cracks you will need get the Mach bike to go at full speed.

Note: You need to beat the champion for Sky Pillar to be reachable.