They're not in there
depends on what your talking about abandoned ship:between dewford and slateport sunken submarine stolen by team aqua/magma just at the front of the entrance to evergrande city
You have to talk to the scientist guy at the ship place in slateport city
First talk to one of the mecanics in the ship building place. He will tell you to find Cap. Stern. Then go to the museum and talk to Cap. Stern that is on the upper floor. Two Team Aqua members will arrive. You will need to defeat them. Then the Team Aqua leader arrives and talks. Leave and Team Aqua will be gone.
a
every where team aqua is or in snoop dogs house.
he is at the top of team aqua HQ, after you beat him you get the master ball
go to the ship town then they will be at the shipyard. first you see a scientist then you see team aqua going back to their base and there you go
How can you find Team Aquas secret base?
you will find team aqua in the under water cavern near the dive point in sootopolis
Team Aqua's hideout
you get it from team aqua
You find them on the summit of Mt. Pyre