My idea is:
You play as a new character in the region of Kanto (before the time of Green/Red/Blue/Yellow.)
Professor Oak has finally captured the legendary Mew. While you are gettign your first pokemon, he releases it in his garden to run around after moths of hard training to make it trust him. Suddenly Team (Rocket maybe?) burst into the garden, in search of Mew. The noise spooks mew and it runs off. P. Oak uses some a Bulbasaur to send the invaders scuttling away. You then recieve your first pokemon (Bulbasaur, Charmander or Squirtle.) and are sent off on a long journey in search of Mew. P. Oak also suggests that you challenge all the gyms to become stronger.
Your rival would be a masked kid that you don't find out the identity of until later.
Team (rocket?) wants Mew to create a new ultra-pokemon because Mew is the ancestor of all Pokemon.
What else could happen? I'm not sure...