You need to Follow Team Aqua to the underwater cave on Route 128
Keep going further into the cave 'till you see Kyogre.
Archie [ Team Aqua's Leader ] will appear and his Red Orb will start shinning
He'll wake up Kyogre and Kyogre will go in a mad stage and leave to the Cave Of Origin.
There'll be some talking and then he'll leave, you leave also. Outside the cave Team Magma will appear and start talking some sence to Archie. Both Teams leave, Steven will appear and he'll tell you to go to Sootopolis. Once you get there, you'll see Steven with Wallace [ yay ]. They'll take you to The Cave Of Origin, where you'll get the chance to catch Kyogre.
There you go again.
Regards, Cameron

thanks for answering my question cameron!

no problem (: