This may not be right but you got to go to Team Aquas hideout you will see a guy who is dressed as a part of team aqua saying jump wailmer jump you head up north to a cave which is where team Aquas hideout is. If you cant get past 2 Team Aqua goons you will have to go to slateport city where the submarine is.
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You don't awaken him until you beat the elite 4. Then go to the weather institute and they will tell you where to go for each Pokemon KYOGRE/GROUDON.
After you get Groudon to settle down, go back to Mt. Pyre or where ever it is he stole it and he returns it and you return your orb as well.
you first need to go to slateport city after you defeated team magma at the Pokemon graveyard.talk to capt. stern and team magma will appear. then go to lilicove city. you can go into team magma s hideout. then go to route 127 or route 128.you need to have dive you can get it from Steve in mossdeep city. on route 127 there will be dark water you can dive in the water. there will be a cave.go inside and defeat team magma. then groudon will awake.then go to the cave of origin and the man will let you in.
You'll have to go into the cave that is just north of them and defeat team Magma/Aqua. Then you might have to fight Groudon/Kyogre. After that they should have moved.
you have to dive where you see a sub you need to go up then team magma Or team aqua will be there go to the last room you will see a groudon or kyogre the bosses will com if it is team magma the boss will glow the blue orb if it is team aqua the boss will glow the red orb then groudon or kyogre will disappear they are at the cave of orgin in sootopolis city go to the cave of orgin there will be steven and Wallace in the way they will talk to you they will bring you to the cave of orgin over there the man is not blocking the way