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