To get the Rayquaza mission, you need to first calm down Groudon. Go to Wintown to see that the ranger leader of Wintown is outside. Talk to her and she will bring you inside and tell a story. She tells you that you need to get to Chris at the temple where you defeated Gordor. You will see the Team Go-Rock Squad Grunts again and some people who want to battle with you. Approach Rayquaza to fight it. Rayquaza is the most difficult Pokemon to catch. The recommended way is to use a golem.