What do you do after beating team aqua at Mt pyre?

depends what version your playing. if sapphire go to slateport city and find captain stern interviewed then team aqua will steal a submarine. you then have to fight them in their lilycove hangout. if emerald go to jagged pass, defeat the grunt in your way if he's there and enter. you will need strength hm to get through here and this is team magmas new hq. in the end you will fight maxie and witness groudon been awakened. after that leave and do what is said above.