It depends.
If you are talking about the one of the coast of Lilycove,then you surf east to get to Mossdeep City.
If you are talking about the one where Archie awakens Kyogre,then you need to go to Sootopolis City and talk to Steven.Then you will find out what to do.:D
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After you defeat team aqua in the underwater sea cavern you can awaken and beat Kyorge. Kyorge is located in the Cave of Origins.
Team Aqua's secret base is located in the lavaridge. Once at the lavaridge you must ride the cable car up to the acro bike. Take the bike and go down the hill. From there you will see a cave, this is the Team Aqua secret base.
you go to mount. chimney go down the side and a new cave will open up and it is a team magma hide out when you beat them go to saleport then when team aqua takes the submarine got back to team aqua hideout and beat them then they will go away also team aqua hideout is where you get a masterball
This is not the team magma cave that is team aqua cave. Team magma cave opens when you have the magma symbol.
go to the top of mt piye, beat all the team aqua up there (but if u have emerald u have to go to firey path and sreach the area and beat, obtian item in the base there, beat maxtie), then go to slatport city, go to the port there and u will see cap'n stern benn interveiwed, talk to him, then you will hear team aqua talking on the mic, go inside and go near team aqua and they will go to their base in lilycove. beat, warp and obtain items in that base(there is a master ball in there somewhere), go outside and the walimar will not be there. Thanks!!