First you have to go to mount pyre and get archie to run to slateport, then chase after him, and then go back to lilycove and raid the base ( don't leave until you get a master ball) then archie will run to an underwater cave. So you have beat the mosdeep gym and get dive from steven at his house then surf to route 128 ( I think) and dive in the dark water. You will face the whole team aqua so be ready, and you also need rock smash and strength. then you'll have to run to sootplis and by lots of ultra balls ( you DO NOT need the master ball). Be sure to save right before facing kyogre so if you beat it or it beats you, you don't have to start all over again.