They went to the hideout. it's east of lillycove city, really close to it... you'll need to surf
In the bay
team aqua boss is in underwater base near soatapolis city and pacidflog town
Go to the submarine and press B. You'll notice you can get up there. If you are above, you'll need to explore a cave with team aqua in it.
The Team Aqua boss is in the Team Aqua Hideout northeast of Lilycove City. You will need the HM move Surf to reach the hideout.
After you find the submarine you use dive up to the surface.
You get it from the cave where Team Aqua has taken the submarine to
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
beat their boss in slaterport
in the back of the base, but they get away with it.
it is in team aqua's base (the one where they had the submarine)
You can find them in the underwater cavern