Go back to the town where you fought for the phantom badge. Go east of the Shop and through the building that separates the routes and cities. You will see a body of water and a cave. Surf on the water and go east. You will get to the next town where the gym is blocked by someone. You have to get the gym open.

Go north of the town. You will have to fight some trainers. You will then see people, a house and a pond. Surf in the pond until you see a gyarados. This gyarados is golden. Fight it and capture it. Then get out of the water and you will see a man with a cape next to a sign. Talk to him and he will disappear. He has returned to the city below. So back to that city.

Go to the house north of the pokemon center. You will see the man with the cape once again. He will show you the secret staircase that leads to the Team Rocket's base. Fight all the Team Rockets,get items and go up the staircase. You will see the black cape man and he will heal your pokemon. Then fight all the rockets until you get to the top floor. Open the door to the room with the bird pokemon and fight the leader. After you beat the leader, go down the fight all the electrodes that are powering the building. You should capture one if you want.