The submarine at the place didnt leave
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1. Defeat the gym leaders on Slateport city, then Lilycove city to Mossdeep city.
2. After that Steven will take you to his house and give you HM Dive.
3. Surf to Route 128.
4. Then dive on Route 127.
5. After you do all that you will find team magma in the underwater cave.
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