Defeat the Elite Four and become Champion
Obtain the Mach Bike
Go to the Sky Pillar on Route 131
Enter the Sky Pillar and make your way to the top
Use the Mach Bike to cross the cracked floors
Save the game before encountering Rayquaza
Interact with Rayquaza at the top to start the battle
Catch Rayquaza with Ultra Balls, Timer Balls, or a Master Ball