I'd prefer an after Bully storyline, say starting after a week of Jimmy taking over Bullworth.
You play as nutjob kid who is new to Bullworth, like Jimmy but instead of meeting Crabblesnitch, you go straight to the Boy's Dorm and wonder who this Jimmy is, you ask Ethan and he takes it the wrong way and fights you, but all the Bullies come and aid Ethan causing you to run away just run far enough and hide in a bin. Simple mission of learning how to walk fight and hide.
Next mission introduces you how to talk to others, unlike Bully you can get into convo's with people. UP is say something positive to what they said and down is to disagree with what they say. Also you can still have taunting and greets. (E.G Do you think this place sucks? UP says Yeah, kinda. DOWN says Not really, I haven't been here long enough to judge yet.)
You have to ask Algie or a nerd about who Jimmy is and get an understanding of how he rules Bullworth.
Next few mission introduce you to the features, like blocking the gangs tagging etc.
Around 10th mission you finally see Jimmy, but because of the characters agression when he speaks, Jimmy thinks he is threatening him, leading to a small cutscene of the main character getting beaten up by most of Bullworth, until the prefects and teachers brake up the fight.
The character is then temporarilly suspended and because he lives in Old Bullworth Vale, chapter 2 opens and a new safehouse.
CHAPTER 2 "The mysterious Bullworthian"
It starts off on Bullworth beach late at night with a cutscene showing a shadowy figure mumbling, "I'll get revenge......"
It goes to the next day when the main character gets a mysterious phone call with an indistinct voice saying "I saw everything, I'll help you get revenge after humiliated me infront of my friends."
I'll think of more later.