John Blake is meant to be a reformed Joker. Let me explain: Joker was the ultimate embodiment of Chaos in The Dark Knight.
Bane is at the opposite end of that spectrum: selfish, Totalitarian Order. In the intervening years between TDK and TDKR there was a power struggle within Gotham's criminal underworld.
In the violence, Joker managed to escape. At the beginning of this movie we will learn that Batman has moved on from his search for the escaped Joker and turned his attention to Catwoman's activities.
I am being a bit vague on purpose--there is so much more going on in this movie than your realize and I do not want to ruin the surprises and shock value.
Rumblings about Catwoman's thefts being related to some larger movement against Gotham reached Joker. To investigate he abandons his traditional look and uses an experimental compound developed by Conti's Roland Daggett to hide his scars.
In this new identity--John Blake--he joins the GPD with the intent of mobilizing them against Bane's League of Shadows.
His motives are in line with those of the comics--Batman is HIS. He does not want Bane to kill the Bat, nor does he want to absolute order that Bane threatens to impose on Gotham.