After the Mt. Pyre encounter in Pokémon Emerald, go to Slateport City. Head to the harbor and trigger the scene with Captain Stern; once Team Aqua takes the submarine, travel to Lilycove City and enter Team Aqua’s Hideout.
What to do next in Pokémon Emerald
- Return to Slateport City. Leave Mt. Pyre and make your way back to Slateport.
- Go to the harbor. Find Captain Stern and complete the story scene in which Team Aqua steals the submarine.
- Head to Lilycove City. Enter Team Aqua’s Hideout to continue pursuing the team.
This is the next story sequence, not a trip to the next Gym. The route order—Mt. Pyre, Slateport, then Lilycove—is reflected in the PKMN.NET Ruby, Sapphire & Emerald walkthrough and the PokeDream Ruby/Sapphire walkthrough.
If the harbor scene does not start
Check that you completed the story encounter at Mt. Pyre’s summit, then return to Slateport Harbor and look for Captain Stern. The walkthroughs establish this intended order, but do not document every possible save-state or event-trigger issue.
Does this route differ by game version?
The steps above are for Pokémon Emerald. Original Ruby and Sapphire, as well as Omega Ruby and Alpha Sapphire, use a broadly similar Slateport-to-Lilycove progression. However, the villain team, orb, and story details vary by version. Follow the names and items shown in your game rather than applying another version’s event wording. The remake sequence is covered in the Pokémon ORAS walkthrough; Serebii outlines the versions’ team and orb distinctions in its Omega Ruby & Alpha Sapphire team guide.
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