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If you are referring to the first Metroid prime, then the underwater ruins you are talking about is probably the Frigate Crash Site. If you look on your map, you will notice that there is a small cavern behind your gunship with a door at the end. This will take you to the Frigate Crash Site. You will need to go underwater to cross the first room. On the other side of the room, there is a door that will lead you to the ruins, which in turn will lead to the Great Tree Hall and Phazon Mines.

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