First clear the game (note u don't get kyogre in soulsilver and u cant get groudon in heartgold but u need both 2 get rayquaza by trading)
Go to Mr. Pokemon to receive the Blue Orb.then get a Pokemon with Rock Climb and one with Surf.At the safari zone route surf and climb until you find a cave.That's the Embedded Tower.Go in and you will see Kyogre.Go up to him and press A. You will ecounter him and then try to catch him.