After you've cleared the hideout, go to Mossdeep, get Dive, and the 7th badge. Then go to Sootopolis (just so you can easily Fly there after the next event is finished). Then at Routes 127-128, there's a long, narrow trench that you can Dive at. There's a cave at the end of the trench. Team Aqua is there, and Archie is trying to awaken Kyogre down there.
And isn't the one you get in Sapphire the Blue Orb? Meh, whatever. The point is that you don't get the second Orb. The Team Aqua Leader steals it and returns it to Mt. Pyre's old couple after Kyogre is defeated (or captured).
God, my hands hurt from typing all that