Im not answering now, or let more guest's answer, because there is no such thing as team aqua.
Villians-
Team Rocket
Team Galactic
go to Lillycove city and then go right to the beach and surf up and then you go into the cave entrance and its really the entrance to team aquas hideout!
use action replay and get the code walk through everything
No
open it
How can you find Team Aquas secret base?
After beating the gym leaders in Mossdeep, go to the Space Center and defeat Team Magma. Then go to Steven's house (which is also in Mossdeep) and he'll give you Dive.
You can't
Capture a pikachu
Unfortunately for you, the Masterball must be obtained when you are in the base the first time. Sorry :(
well you go swim then find the dark spot of the largest sea then face the same pokemon then catch it,the battle team aquas
you go to the team aquas submarine then use dive then your in sea floor cavern and make sure you battle everyone
beat the team aqua base