Instructions
Finish the game and wait for the bonus missions after the credits. Defeat Kyogre and Groudon. Pursue the third mission after Groudon by going to Wintown and accepting the mission from Elita.
Enter the temple, and defeat the three Ekans that await; save the game. Capture Ralts, Kirlia, and Gardevoir in the same area, then capture all the Pokemon you can as you make your way through the level. You should have about seven Pokemon caught before proceeding further. Save the game.
Exit the chamber and climb up the pyramid. Defeat the Solrock and Swellow that meet you there without using the Pokemon you just caught; save them for fighting Rayquaza. Climb to the summit and encounter Rayquaza.
Fight Rayquaza. Strike after he stops firing thunderbolts. Use Umbreon first, then Gengar if Umbreon is defeated. Work fast, making sure to use Gengar's ghosts to stop Rayquaza's cyclones before they hit. With diligence, and attacking Rayquaza whenever it pauses in action, Rayquaza will be defeated.