Here is how I would do another game...take a cue from Nolan call it something like The Fall of The Dark Knight.
Set it a couple of years after AC, I'd take the main antagonist straight out of the current books, The Court of Owls. The writers are killing it with that storyline right now, The Court are out to take over Gotham. Publicly, through dummy corporations and the like and through the criminal underworld.
Bats is still in a funk over the Joker's death and kinda phoning it in night after night, all those secondary villains and their gangs are thriving but keeping it low key to try and avoid bringing Batman back full time. Nightwing, Red Robin and Batgirl are picking up the slack with Oracles help but they just aren't the world's greatest detective.
What better way to pull him back into the game than the same thing that took him out, The Joker, multiple sightings of the Joker (with Clayface still locked up tight in AA) send him back onto the streets. For this 'prologue' mission I would pull the villain outta the current books too and make it The Dollmaker impersonating Joker. Have Harley come out of the shadows after beating him and mock him for how much the Joker has effected him and tell him he can't even see what's happening in his precious city, hinting at the new power taking over that will set him on the trail of the Court.
That would set up the main story of tracing and tracking the Court with them coming at him through proxies like Black Mask, Two Face etc and their Talon assassins of course. I would have a branching side story, like Catwoman's, but bigger involving a public attack on Wayne Enterprises that he blows off because of being too focused on the Court and 'his' city. Have that side played through with Red Robin and Batgirl with help from Oracle. IF it were to have co-op I would make it Nightwing, Dick is his oldest alley and after Alfred his closet friend, he would be able to get through to him and convince him he needed help.
I would have the story focus on breaking Batman, removing his ally's off the board. This could be a cool way to introduce some new villains to the series too. Who better to take out Comm Gordon than his serial killer son James. The Red Hood could take out Red Robin, someone who used to be Robin driven to the ultimate act of revenge by Batman being more broken by the death of the Joker, the man who killed him, than his own death. By take out I mean incapacitate not kill.
The Court has always been ran by some of Gothams most powerful families, so as the two story lines come together they realize that someone knows Batman is Bruce Wayne and the only person left alive who knows that just happens to be the last surviving member of one of Gothams most wealthy and powerful families, Tommy Elliot aka Hush. You could even bring back Talia as the mastermind behind the whole thing in revenge for his betraying her in AC, not like she doesn't know what a lazurus pit is.
And then just when you think he can't be broken down anymore 'Hello father...' which in that classic comic book reversal could also be the thing that pulls him back from the brink, with Nightwings help, rescuing his son from the League of Assassins.
Yes I am aware I spent way too much time thinking about this but in my defense I did just work a boring ass 16 hour shift at the hospital