I beat the Elite 4 and when I returned to the Cave of Origin hoping to catch Kyogre after I knocked it out the first time it was there. Do I need to beat the Elite 4 a second time as so far I only beat them once?
It is in a different cave in the cave of origin. Not the one where you battle it originally. I forgot which cave it was in, sadly, but I know it is in the Cave of Origin. Hope I helped!