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You should go to the top of the Mt.Pyre first (outer part). you will meet Archie, then after some talking, you get a Magma Emblem (This is a very important item of the storyline). Then you should fly to Slateport City. You should ran into a crowd around the shipyard, talk to the scientist next to the reporter. Then after some talking and story, the submarine is stolen. Then you go back to the beach of Lilycove, then move north into the Team Aqua Base. After you get rid of the Team Aqua member guarding the Submarine, Archie ran away with the Submarine. Then you get out of the base, your path to Mossdeep should be cleared now.

p/s: Explore the base before looking for the submarine and you with find a Master Ball in a room with 1 nugget and 2 Electrode.

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