Instructions
Add an Ice, Rock or Dragon Pokemon to your team of six Pokemon. Return to the "Sky Pillar;" it is marked on the map if you've forgotten the location. Follow the stairs up to the fourth floor.
Select "Mach Bike" from the "Start" menu and ride the bike across the crumbling fourth floor, then go up the last set of stairs to find Rayquaza. Save the game. Walk up to Rayquaza and press "A" to begin the fight.
Press "Start" to access the menu screen and the list of available attacks. Put Rayquaza to sleep using "Hypnosis" or "Electric" attacks by scrolling through the menu using the control pad and selecting the attacks by pressing "A." Use powerful attacks to steadily decrease Rayquaza's health.
Throw an "Ultra Ball" by selecting it from the "Start" menu and pressing "A" once Rayquaza's health is in the red zone and he is paralyzed or asleep. Continue throwing "Ultra Balls" at him if it doesn't work the first time. Restart from your save point if you run out of "Ultra Balls" to try again.