Get A Masterball To Catch Kyogre:

When you face Team Aqua in Lilycove city. Don't talk to the woman at the submarine, yet. done in the bottom right hand screen should be a teleporter. Go on it and it'll take you to a place full of them try out each one until you get to a room with four poke-balls. get the back 2 and you will get a NUGGET and a master-ball.