Just an Idea, but;
You start out in the Starting town, Your Mother sends you out to go find the Pokémon Professor. You find a Messenger who's being attacked by Thugs. You Interrupt them, and they flee with some of the Messengers parcels. As you peruse them the Thugs drop a parcel containing three Pokéball, each one containing a starters. You catch up to the thugs in their hideout in the woods. A battle breaks out and your win back the rest of the parcels. You meet back up with the Postman, he then takes you to the Poké Prof. The Professor then thanks you, mentions how much the one Pokémon you choose has developed a bond with you, and asks if you would like to to do a great favor for Him/Her. The Favor is if you could obtain the information of all the Pokémon of the Region.