The city is mourning the loss of their hero. Blake sees the sadness in his orphans over witnessing what happened that day on the bridge. Although Batman has saved Gotham it doesn't take back what they lost. Someone they believed in and held faith in.
Meanwhile, Gordon with Blake's help start to oversee the construction of holding cells to house the recaptured villains who Bane broke out. Blake does not take on the Batman costume yet, instead opting for a guise very similar to Bruce's pre-Batman. The city doesn't have any clue that this is going on and they keep it that way. Blake is also very adamant about not being Batman at this point so the villains aren't confused. This is someone new.
Meanwhile, a new criminal element rises spearheaded by Black Mask. He threatens the city by mocking that their hero is dead and gone and they have no one to save them.
Blake, having seen this decides that he has to come back and be the symbol that Gotham needs however hesitant about it. Gordon too is hesitant. Blake tells him that he is also, but the city needs hope. He goes to stop a crime as Batman and is caught on camera signaling his return.
Black Mask is taken in by the footage because he knows Batman from the time in-between BATMAN BEGINS and THE DARK KNIGHT and knows this man couldn't be Batman. He furthers his organization and brainwashes civilians into joining his growing cult (never called the 'false facers') proclaiming that the replacement can't be Batman.
Blake starts to doubt himself. And Alfred, having also seen the footage, returns to the cave where he questions Blake about what he's doing, why he's doing it and if he's ready for what he signed on for. He doesn't give any hints that he knows that Bruce is alive. He just tells him that Bruce was always looking for someone to take up the mantle. Blake tells him that sometimes he is uncertain if he is that guy. Alfred helps to guide him and by the end naturally becomes a sort of surrogate father figure to him (to match this we also see Blake becoming a father figure to the orphans).
With Alfred's and Gordon's help, Blake takes on the mantle of Batman. The city starts to regain it's hope and faith as they see Batman has risen from the ashes to protect them once again. He fights Black Mask in a populated area of Gotham City for everyone to see. He's about to kill him with his fists when he stops. Black Mask asks him why. Blake merely tells him, "
I'm Batman." Black Mask mocks him that he never will be.
Blake tells Alfred that for everyone else he'll be the Batman, but to him he can't completely be and needs to do things his own way. He is okay with being Batman's replacement and wants to carve out his own legacy as well. Alfred accepts that and tells him he'll help in any way that he can. Knowing that the mansion is not suitable for the manor because of the orphaned and at risk youth, Blake relocates it to another Wayne estate similar to the penthouse.
Gordon, with the city seeing Batman's return, lights the bat-symbol up into the sky. Bruce, with Salina, sees the inauguration of lighting it up and smiles knowing that Blake is finally ready.
Plus - one of the at risk children? Jason Todd. Along the way he becomes more and more suspicious of Blake and Blake notices this and ultimately this is why he relocates the batcave out of the mansion. However, the sequel will see the repercussions of this.
In the finale (of the Blake trilogy) Bruce Wayne
will return just like he did in the comics. And for those who didn't catch on, yes - a lot of the above is inspired by Dick Grayson's Batman arc. I really think they have a lot going for them, and like Batman Year One being Batman Begins & Knightfall and No Man's Land being The Dark Knight Rises, this should be heavily comics inspired with a real world grounding in it.
Many will be tempted to have Bruce come in earlier, but I think that is way too much. You need time to acclimate to Blake taking on the mantle. Bruce will appear somewhat in a sequel and definitively in the final chapter. In the final chapter, Blake will become Nightwing, Todd will become Robin, and Bruce will become a Batman who acts only when it is essential leaving most of it up to his younger proteges who he has become more of a mentor of - imagine a younger Batman Beyond kind of Bruce Wayne and you've got it.
Also the plot should in some way reflect the audience adjusting to Blake in the costume. Thus, having the film be about that adjustment - it works. Also going along with the christ-like allegories from the past that people pointed out to... resurrection. Every time I see that bus filled with children chanting "Batman!" I don't see them as being able to really understand Batman dying - to them it's still a hard tragedy. Because what Batman has meant for them has gone. They need someone. And that would serve as Blake's main motivator. He is their champion just like Bruce was to him.
Basically, JUST REPEAT WHAT THE COMICS DID - BUT DIFFERENT.
Just like...
BATMAN BEGINS - BATMAN YEAR ONE, THE MAN WHO FALLS.
THE DARK KNIGHT RISES - KNIGHTFALL, BATMAN: NO MAN'S LAND.
For those claiming "it ruins retirement" for Bruce to be brought back like that in the end. Not really. I'd still see him with Salina, living peacefully with Alfred, and enjoying himself from time to time like his 'good old days' which by that point he would start to miss. In a degree, he'd be like an Alfred who can really help them solve things, be proactive, and once in a while do field work. To me, that's still a retirement and true to Batman all the way around. I can't see him forever hanging up the cape so to speak, but rather stepping back mostly to leave it to the younger generation to continue his legacy. I didn't see Bruce as anything but really 'retired' in Batman Beyond.
Also, as said, I definitely agree with those who have said bringing Bruce back immediately is the wrong way to go. One scene at the end of the sequel, perhaps two in the second sequel, then bring him back for everything to come full circle in the end of the second trilogy. Or one scene in the sequel, none in the second sequel, then his return in the end of the second act of the final sequel. The focus should instead be on Blake and Gotham and legacy. The way Blake, the mansion, and the boy's home have been set up? It definitely lends itself to a younger orphaned or at-risk Robin stumbling upon Blake's secret. Nolan left us with A LOT.