if it were me, here's how i would've included joker in the plot :
it would kind of be a mixture of sorts between things like dark knight returns, no man's land and arkham city.
for starters , just as in dark knight returns where joker was sitting in arkham catatonic for years waiting for batman to come back, the same thing would be what i would've done in rises. although i would've basically had everyone underestimate the joker even more so in rises.
it's been 8 years, and he's been locked up doing absolutely nothing, so at this point most of gotham think of him more as a joke. i would've had his first scene to be him in arkham being interviewed by a reporter without makeup, somewhat similar to how they interviewed charles manson when they captured him. so the reporter is basically being a total dick to him, asking him all sorts of questions like how he must feel knowing that batman's back or knowing that he's lost his respect as a criminal mastermind. things just to get joker really pissed off. not a good idea.so then joker starts messing with him back, asking him things like how it must feel to have a wife who's probably cheating on him as they speak, etc. which then causes the reporter to ask " well, what about you then ? you got a girl here ? " and the joker would respond , in sort of an in your face smartassy way " as a matter of fact i do... my psychiatrist " .
so the reporter would ask " oh ? and how do you think she feels about you ? " to which the joker replies " why not ask her yourself ? she's right behind ya. " and then harley quinn would be behind the reporter , and she'd kill the reporter as the joker watches smiling and giggling.
so harley breaks joker out , right around the time all the destruction caused by bane starts happening, so joker seems to enjoy the state of gotham, being able to kill randomly and more freely than ever. only thing is, he's pissed off that he isn't the one causing all the destruction. and he's also pissed that bane was the one to get to reveal the truth of harvey dent instead of him, as well as the fact that bane is responsible for batman's current grief in the movie.
so joker does a speech in front of arkham on top of his "slaughter is the best medicine" truck, as a way to mock bane's speech in front of blackgate, telling gotham how HE was the one who caused harvey dent's downfall and that bane should've " given credit where credit is due " , and breaks everyone in arkham out and him and harley basically start their own little army against bane, to show him " how chaos is really done " . so now it's an all out war ( as if it wasn't already, lol )so joker would have his own section and army in the city, while bane has his and gordon has his cops.
so , similarly to no man's land, joker would kidnap all of gotham's babies in an effort to regain batman's attention, only at this point batman's busy dealing with bane in the riot in the middle of town and all, so he's waiting and waiting for batman to show up and eventually he gets fed up and realizes he's not coming so he leaves harley to watch over the captured babies while he takes matters into his own hands. then i'd have catwoman go after harley while joker goes to find batman and kills bane , similarly to the video posted earlier.
in one last attempt to have his " fun " with batman , joker challenges him to a " race " to see who'd get to the nuclear bomb first, and he chases after talia's truck in his own slaughter truck while batman's also trying to stop her, and like in the movie, the truck would crash , yada yada yada, but then batman would try to get rid of the bomb, only to have joker attacking him trying to stop him from doing that , as he feels it'd be " poetic " to have their last fight as they and everyone else in gotham's about to be blown to hell, they duke it out, joker gets stopped at gunpoint by gordon, then like in the movie batman takes care of the bomb, as joker looks over at the explosion , realizing he'll never get to have any " fun " again, so he takes out his signature knife and uses it to kill himself.
so basically joker spends the majority of the movie trying to regain his status in gotham and also trying to get batsy's attention again.
now, this could all be a terrible idea, and you could all say " **** fanboy, don't ever write for movies" , or maybe some would like it. i don't really care, it was just a random bunch of ideas that popped into my head and i felt like getting them out. and i also realize the movie would have to be quite a bit longer to fit all this in as well, lol