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After the player visits the summit of Mt. Pyre for the first time (and, in Emerald, also clears the Magma Hideout), Captain Stern is seen being interviewed outside the Harbor. Submarine Explorer 1 is then stolen by Team AquaSEAS/Team MagmaROR.

Until Team Aqua steals the submarine at Slateport City, two grunts will block access to the rest of the hideout from the entrance.

After going to Mt. Pyre and clearing the Magma Hideout, go to the Harbor in Slateport city.

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Yes I already did that I'm at the part where groudon kyogre fight in sootopilis city
If you've already seen them fight, the doesn't that mean you've already been inside Aqua Hideout? Are you sure you're playing Emerald?
Yes I'm playing emerald  I went on serribi and found team magma's hideout
Did you already get inside the Aqua Hideout?
Yes I'm on the elite 4 right now