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They were there when I first got to Slateport City, but they were gone after 10 minutes in which I did nothing that seemed storyline-advancing.

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All I can find on this is the actual skipping part, which involves getting the letter to Steven without getting flash, which lets you skip the gym and go to Slateport, with which you can move from there with the whole getting the ship part to the captain which triggers the aqua grunts going into the museum, etc.
Luna, I'm going to edit this and make your comment seem off-topic. Sorry.
Did you give the ship captain the Devon parts? I believe that's what makes the grunts move
No, the ship captain is inside the museum, so I couldn't do it until they moved away.

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In order to make the Aqua grunts move you have to go into the Shipyard and talk to the person behind the first table. He will then tell you that the ship captain is in the museum and when you go back there will be no grunts in the way

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