they don't go anywhere.they go back in the hiding spot or hideout then they don't do anything until ARCHIE strikes again.
The Magma Base doesn't exist in Sapphire Version, but the team Aqua's Base is located outside of Lilycove City.
Pokemon Ruby= Magma Hideout at Lilycove Shore Pokemon Sapphire/Emerald= Aqua Hideout at Lilycove Shove Pokemon Diamond/Pearl= After you beat Cyrus at Veilstone City
Staleport City and LilyCove City
Lilycove City.
there is none
South from lilycove city.
You have to surf from LILYCOVE city to the right
lilycove city
in lilycove city north part of the city
in the cave where team magma escapes you in the submarine next to lilycove city
move deleter in lilycove city
in tge cave just out of lilycove city