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If you have seen Team Magma/Aqua go off with the sub, use your Pok?nav to comb through the big stretch of ocean til you find a section marked "Underwater Cavern" go to it and use dive on the deep spot, and surface inside somewhere to get to the hideout. Finish it, and then you can enter the Cave of Origin in Sootpolis.
From Mossdeep City you keep going south till you hit Route 128, just keep going down till you see a spot that looks kind of like a circle (you can walk around on it), have your one of your pokemon use dive on the out side if the circle. Then you will see a cave go in then your at the sub.