GETTING WATERFALL:
In MOSSDEEP CITY go to Steven Stone's house, which is North of the City.
In there he'll give you Waterfall, but you must beat the GYM LEADER[S] first.

GETTING TO EVERGRANDE CITY:
EVERGRANDE CITY is located all the way East of Route128.
Again you'll need HM Waterfall for this.

GETTING TO CAVE OF ORIGIN:
You'll need to follow Team Aqua\Magma to an underwater cave on Route 128
There you'll encounter Kyogre\Groundon[ though you won't be able to catch it ].
You'll have to Battle Maxi\Archie, he'll try to control Kyogre\Groundon with his
Red\Blue Orb.
Kyogre\Groundon will go into a madstage and leave to CAVE OF ORIGIN.
Go to Sootopolis City and enter CAVE OF ORIGIN.

Regards,
Cameron.