what do i need to do to be able to battle the third gym leader?
You've already tried entering the gym, right? and the leader left and went off somewhere? You have to go to the main dock (the one in the center) and follow the dialogue with the Plasma grunt, then head back to the gym area and follow Belle/leader/Iris near a Plasma building, and defeat a grunt or two.
Edit: What level does Meguroko -> Warubiru?