Did you check all the doors before coming all the way down? One of them should have been blocked off with rocks before you encountered Kyogre the first time. Now, after you have seen Kyogre, go through that door. It should be a free path. Take that path all the way and you should see another door. Enter that , and you should be back to where Kyogre is. If there are more doors, just check each one. I haven't been there for a long time, so I forgot which door it was (If there are anymore) If the path is still blocked off, I don't know what else to tell you but reset. Hope you have good luck!