Ok. This might help:
› After you get HM Cut and leave the ship, you can't board the S.S. Anne any more. If you beat the Cinnabar Island Gym (the seventh Gym), you go to 1, 2, and 3 Islands. But you do not actually go in the ship. Later in the game, after you help Celio get the Ruby and Sapphire for his machine, he gives you acces to 4, 5, 6, and 7 Islands. He also enables the ability to trade to the third generation games (Ruby, Sapphire, and Emerald).