Heres my idead:
You are on top ten most wanted on the F.P.T.I. (Federal Pokemon Theif Inspectors) and have just graduated from trainer school with a bagon as a gift to see to police waiting outside for you. They confront you for stealing pokemon and bring you to prison. You have to climb through the vent and find your bagon, and run outside to get picked up by a team rocket helicopter. You change into your uniform and start your first mission.