How to Get Rayquaza

1.  Have Groudon and Kyogre already and have them in your FIRST 2 slots of your party and talk to the woman inside the red house near the Gym in Crescent Island

2.   After you talk to her, you should have the Meteorite Shard. Now that you have the meteorite shard, fly to Anthian City and go to the Park District. Once you're in the park district, walk to this area circled in the image below and a cutscene will begin. 

TO GET MEGA RAYQUAZA, LEARN THE MOVE “DRAGON ASCENT” IN COLOSSEUM.