Instructions
Finish all of the other missions in "Blue Team" or "Red Team." The Sky Tower is the final story mission in the game.
Select the Sky Tower dungeon from your mission list. Xatu will then give you the Teleport Gem needed to enter the first floor of the Sky Tower.
Battle and climb your way up 34 floors in the Sky Tower. Train your Pokemon to level 30 or higher so they will have a chance against the savage Aerodactyls, Tropius and Metagross that live in the tower. Sky Tower is sectioned off into 25 lower floors and nine top floors.
Enter the ninth level on the tower's top to fight Rayquaza. Rayquaza is a level 45 Dragon and Flying-type Pokemon that uses savage attacks like "Dragon Claw."
Hit Rayquaza with Ice, Rock and Dragon-type attacks to severely damage it. Use a Sleep Seed to force Rayquaza into a nap. This lets you inflict serious damage to the beast without worrying about being attacked in return. When Rayquaza wakes, use another Sleep Seed. Rayquaza will be defeated after you chip away its large health meter of 600hp.