i don't exactly know because i don't play Pokemon ruby sapphire and emerald i only play Pokemon games for the ''ds'' like Pokemon black and white not for ''game boy advance'' like Pokemon ruby sapphire and emerald
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there is no sub. only on Pokemon sapphiere and emerald. you have to defeat Team Magma, not Team Aqua.
first, defeat the last team magma member in mt. pyre and talk to the old man in there and you will get a magma emblem and the go to lavaridge town and go up the mountain and you will see a team magma member and fight him and then your in their hideout.
First, you have to defeat the Aqua team at Mount Prye, then you have to defeat the Magma team at their hideout near Lavaridge. Then, the guard will be gone.
This is not the team magma cave that is team aqua cave. Team magma cave opens when you have the magma symbol.
Team Aqua/Magma took it underwater. Dive a look around for a secret entrance underwater and go in it. You will see the submarine. Then one you are at the sub, go up to the surface above it and defeat team Aqua/Magma.