Probably Making a Mark.
The final chapter starts off with everyone pretty much kissing Jimmy's ass, letting him know he's on top of the school. He's so full of himself, so out of it. He's ridiculously cocky, easily provoked to go and leave his tag on the freaking Town Hall.
First time I played it, I was so unsure what to expect. When I got into the dorm, and saw Pete sitting on the floor of Jimmy's room with his back to the door, this awesome feeling of just knowing that something isn't right took me over.
Mission ends and you're in a worse position than you joined.
Best part is that you get to beat up people without feeling guilty about it, because they're quite the hostile fucks themselves.
Go see the principal too, for the same reason. I guess I just like plot twists.