After defeating the Elite Four, go to the Weather Institute and talk to the professor on the second floor. He will say there is a heavy rainfall in a certain route. Get to that route. There must be any place to dive that was not there before. Dive and get to Kyogre. After you catch Kyogre, go to the weather institute and talk again to the professor on the second floor. This time the route he will say will be on land. Get to the certain route. There has to be a cave that was not before. Get inside the cave and find Groudon.