you beat the team aqua people at Mt. Pype and then go to livicove and surf at the beach to a cave.Go into it and that is how you do it.
No
open it
How can you find Team Aquas secret base?
You can't
Capture a pikachu
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
beat the team aqua base
there on the mount after the lady that sells lava cookies if you have the badge it will open automaticaly
Team aquas base where they first hide the submarine. It's in one of the rooms
Keep progressing in the game and you will find it. East of Lilycove city.
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!
Their base is always at Lilycove, but you can find them other places (Mt. Pyre, Underwater Cavern, etc...).