The only thing u can do is in s rank is go in battle week it starts on Monday and u talk to the main person in the battle club and he will start a dialogue that u reached s rank and will give u access to the door behind him
Is there anything to do in the base of operations after u defeat Giovanni and are locked out of both Magma and aqua headquarters cause it's telling me team magma leader is not here for the meeting
You can take over teamrocket by going inside the team rocket hideout(Southern district) acting like a team rocket grunt and choosing more power and money when Giovanni gives u the choice then you have to defeat him to take over team rocket