Instructions
Jump twice and press the dodge button in mid-air to avoid Rayquaza's first attack pattern. The first attack is either Iron Tail if you are close to him or swooping across the screen at you if you are far from him.
Dodge or defend against Rayquaza's second attack string which is always either Hyper Beam, Extreme Speed or Dig. Double-Jump out of the way of Hyper Beam and Extreme Speed. Press your Shield button when Rayquaza dives into the ground to perform Dig and run to the other side of the stage before he pops back up.
Dodge or shield against Rayquaza's third attack pattern, which is always either Fly, Confusion or Thunder. Walk to the other side of the screen when Rayquaza flies to the top to perform Fly. Press the Shield button when Rayquaza's eyes glow red for the Confusion attack. Jump across the screen and press dodge in mid-air just as Rayquaza's Thunder attack hits to avoid it.
Attack Rayquaza with your strongest attacks whenever you are not defending against his attacks. Rayquaza always attacks in a pattern of three, so attack relentlessly until he makes his move then focus on defense.
Repeat this strategy until you have completely lowered Rayquaza's health points.