Firstly, you need the MAGMA EMBLEM, you get this by defeating all team magma members in Mt .Chimney then a old lady will give you red orb. So then you can now go to the jagged pass and with your magma emblem; you can go in and defeat team magma then you have to beat MAXIE he is hard. Then after you do that you go to Lilycove City and you see a cave and the guards will be gone so you can go through.
All of this does not make sense, so I will tell you the real way. First you must have beaten magma hideout at Mount Chimney. After that you must go to aqua hideout in Lillycove City. The two grunts will say the their boss went to Slateport to steal a submarine. Once you get to Slateport, go to the ship yard where you will find Captain Stern getting interviewed by gabby. Go up to her and press A. The interview will end and then team aqua will come on the loud speaker. Then Captain Stern will take you in the shipyard and team aqua will take the submarine. Then fly back to Aqua hideout and and the two guards will be gone. You must then find your way through the Aqua maze. Then you will face aqua boss. I forget where but on the teleporter mats if you pick the right way, you will find two level 30 electrodes guarding a master ball and a nugget.
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Go to slateport first and go to where they are unveiling the new ship. Team Aqua will be stealing the submarine and after they steal it, go back to lilycove. The two sentries will be gone and you may pass into the hideout.
YOU CANT BECAUSE WANTS YOU LEAVE IT SEALS UP FOR GOOD I KNOW BECAUSE IT HAPPEND TO ME IN RUBY KNOW I DONT HAVE A MASTER BALL. BUT THAT DIDNT STOP ME I STILL CAUGHT ALL THE LEGENDARY POKEMON p.s. the master ball is in that cave
first go to slateport harbor ...you will see captain stern taking an interview.then you are going to run inside...your going to see team aqua.after that go to the hideout