Well, here is the skinny...
You have completed the Kanto League and Sevii Islands story, Oak summons you to his lab, he asks to give you a starter (Charmander, Squirtle, Bulbasaur), because he wants to see them grow by your side again, he then tells you that you can go to Johto and see all the Pokemon there, so, he gives you a ticket and lets you ride on a ship...
So, just imagine Johto three years earlier than HGSS, with the "old, creaky radio tower", a cycling road and more.