Idea for how/where you encounter Baddon. You've just moved to Pallet Town and there are a couple of boxes yet to be unpacked lying around. Whenever you speak to your mother she always end the conversation saying to keep away from the box in the corner, no matter what the conversation was about. Interact with the box and a message saying 'It's filled with strange leather clothing and what appears to be a swing set', yet nothing happens. Later on in the game you get a Key Item that awakens your mom's dildos in the box, allowing Baddon to be challenged. I dunno what the item is, it needs to be something related to the mother being a whore with living dildos.
Another anon posted this in a prior thread, I reckon it'd be a good theme for the Baddon fight.
http://www.youtube.com/watch?v=iKB4S1Vf3oY 