First talk to one of the mecanics in the ship building place. He will tell you to find Cap. Stern. Then go to the museum and talk to Cap. Stern that is on the upper floor. Two Team Aqua members will arrive. You will need to defeat them. Then the Team Aqua leader arrives and talks. Leave and Team Aqua will be gone.
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You need to get past the Team Aqua grunts at Lilycove Town to advance on Pokemon Emerald. In order to do this, you first have to beat Team Aqua grunts at Lilycove Town.
Go to Mt. Pyre. Stop Team Aqua. A woman will give you the Magma Emblem. Go to the Jagged Pass. The floor will rumble and a door will open. Go there. That's Team Magma's hideout. Battle Maxie. Then go to Slateport. Team Aqua will steal the submarine. Then you can finally go to Team Aqua's hideout. (A master ball is there) And fight the executive. Then the Wailmers are finally gone.
First you have to deafeat Team Magma In Mount Chimney. Then go to slateport city to the dock building where you run into team aqua stealing a submarine, then you go to Lilycove and enter Shoal Cave. The two Team Aqua Grunts won't be there any more so you can pass through. Fight all of Team Aqua and The person Team Aqua Grunt that was training will not be there any more so you can surf past them. Keep surfing until you get to Mossdeep and Mossdeep is a Diffrent Story.
You have to give the scanner to the prof. who makes ships and then team aqua will show up inside the ship house something and go inside the submarine then go to lily-cove city then go to the city sower.
Easy, Once you obtain the "goods" form the Devon Head, travel back South past the Forest between Petalburg and Rustboro. Between Petalburg and The petalburg forest is Mr. Britneys House. Mr Britney owns a Boat which you can use to travel to Dewford - Just talk to Mr. Britney in his house. In the Cave to the Northwest in Dewford, A man named STEVEN is waiting for his letter. once you give the letter to STEVEN return to Mr. Britney who is waiting at the pier in Dewford. He will take you to SLATEPORT city. Once in slateport, Travel North to the Slateport Museum. Inside, Team Aqua has taken over. Go upstairs and CPT. Stern is waiting for his goods. Talk to him, then battle the Aqua members. You have delivered the goods ;)