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head back to Slateport City. (City with Ocean Museum). Go to the pier North

East of the town. You will find a crowd there.Talk to the Capt Slate and enter the building. You will see the leader of Team Aqua (You do not fight him this time though), and he will escape using a submarine. After you have done all of the above, now head to Lilicove City. Go to the Dept store in the North of the city. You'll find your rival waiting there. Defeat Him/Her, and head to the eastern part of the town which is a coast.Use Surf to the north and you'll see a cave which is the base of Team Aqua.Enter and beat the living daylight of them. Make sure you get the Master ball. Once you've beaten the leader, you'll never be able to get back to this place again.

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Q: What to do after mt pyre on sapphire?
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On top of Mt. Pyre


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