It took me a while to figure out, but go to the big wooden house at the south-east side of the Slateport. Inside there is a kinda bold man who you need to talk to, he will ask you to find Capt. Stern ... and then you can go in. :P
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Go In Stern's Shipyard At Slateport City And Talk To An Old Man Named Dock
First talk to both of them. then go to slateport. go to the slateport harborand then interesting things will happen then the guards will be gone.
To bad.... I have that problem too....
Captain will be waiting in Slateport go back and talk to them him. Afterwards the Headquarters of Team Aqua/Magma will be open.
you first need to go to slateport city after you defeated team magma at the Pokemon graveyard.talk to capt. stern and team magma will appear. then go to lilicove city. you can go into team magma s hideout. then go to route 127 or route 128.you need to have dive you can get it from Steve in mossdeep city. on route 127 there will be dark water you can dive in the water. there will be a cave.go inside and defeat team magma. then groudon will awake.then go to the cave of origin and the man will let you in.