Go to slateport city and visit the crowd then come back and visit the aqua base.
go to slateport and go to the harbour
Talk to the remaining aqua member in the museum in slateport city.
then they will be at there hideout in lilycove city or if not there then at the slateport harbor
A team aqua grunt gives it to you in the slateport museum after you defeat them all.
Capt. Stern is in the Museum where all the the Aqua/Magma members are conjugated around.
Theif can be obtained after beating team aqua in the ocean museum in slateport city, just talk to the team aqua member that's still inside and he will give you thief.
beat them at their lilycove cave hideout. then go to slateport harbour. and then to the seafloor cavern
You have to talk to the scientist guy at the ship place in slateport city
TEAM MAGMA GOES TO THEIR HIDEOUT IN THE JAGGED PASS.TEAM AQUA GOES TO SLATEPORT CITY TO STEAL CAPT STERN'S SUBMARINE.
you go to slateport city and go to the place where the boat is and you will see a group of people. go inside and you will see the boss. then go back to lilycove and go to team aqua's hideout and you can go inside.
Captain will be waiting in Slateport go back and talk to them him. Afterwards the Headquarters of Team Aqua/Magma will be open.