Ok so this is how I think to round out the trilogy for the Nolan Batman. Ras Al Ghul found the Joker and taught him to be evil. He taught him like he did batman only reversed. He erased his Identity and such, removing DNA fingerprints, records etc., since the LOS can do that, since they've infiltrated "everything" Ras released him into Gotham to antagonize Batman.
So it's not really how to round it out, but hidden behind the Dark Knight that they could work with.

What do you think ?

The only thing with that is that the Ras of the Nolan universe isn't really a 'bad' guy.
Yeah. He is a villain, but his intention is to destroy the evil in Gotham not cause more.
I mean, he trained Bruce with the intent of him leading the ninjas into Gotham and destroying the criminals.
And everything with the fear toxin was to turn Gotham against and destroy its self. Thus getting rid of the criminal problem in Gotham.

While it's in interesting idea, it doesn't fit with Ras' motive for this universe.