When you beat them in the radio tower go to the Underground Tunnel and the door that was locked before you can now unlock. Go in there, beat the Rocket Grunts, and talk to the captured director. He will give you a key that you use to unlock another door in the radio tower which leads to several Rocket Executives. Beat them and them you can go wherever you want. But if you've already done that go to Mahogany and beat that Gym Leader.
