(spoiler) The Jokers Death at the end of Arkham City meaning Batman could be looking for a new angle, a new villain and we here at WhatCulture towers are here to offer a few ways they could do this with a few select story ideas...
1. Return Of The Joker
The Story: The villains of Arkham City start appearing throughout Gotham after the Citys controversial final plan means all of Gothams super villains are released under compassionate grounds (or some other form of convenient government mishandling that aid the narrative) and, predictably, start wreaking havoc on the residents. As Batman it is your duty to stop and apprehend these villains who are destroying Gotham but as you do that a plan starts to become apparent; the spots of destruction arent random enough to be these criminals working without plan. Who is behind it? Well...I think you see where this is going. The Joker has managed to fake his own death to stop Batman worrying about him whilst in the mean time convincing all of Gothams criminals to work in a co-ordinated manner to best destroy the Batman and then take Gothams soul with it.
Awesome Moment: Batmans captured and beaten and The Boss stands over him. Through his bleary vision the face comes down to say hello and its The Joker.
Reason This Should Be The Story: The Joker has been a vibrant, funny and destructive delight in the last two games and it would be sad to see him go.
Reason This Shouldnt Be The Story: Batman has enough brilliant villains to be able to get around the gap The Joker will leave, and going back to a Joker villain would be a bit of a safe journey for Rocksteady.