The first two Nolan Batman movies were about Bruce's faith in the people of Gotham (and the goodness of humans in general):

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Batman Begins

He left the League Of Shadows because he was against killing people, and told Ras "there are good people here" in Gotham, when Ras tried to destroy it.

The Dark Knight

On the ferries, we saw that this was in fact true, even among the criminals Bruce fights! But at the same time, we also saw that even the best person (well, maybe Harvey was second best) can turn bad.

which brings us to...

(New title:) The Caped Crusader

We have Catwoman showing the reverse of Twoface's arc (that a hardened criminal can be fully redeemed), while we also see the city as a whole demonstrate that it has grown, to the point of no longer needing Batman, by fighting back against it's most massive threat: Bane and his team.

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Bane's plan: blow all the bridges, take over the city, rule it as a king, and use the constant threat of his huge bomb to keep anyone from doing anything about it inside or out (kinda like North Korea does irl).

Batman is effective at slowing this plan (even when they are helped by Catwoman, who has her own reasons for fighting Batman that we'll learn later), until a scene where Bane's team discovers Batman's secret identity (as a result of the difficulties/complications of still being chased by the police since the last movie), giving them the upper hand that they need to take him out.

Bane uses this knowledge to set a trap for him, forcing him to a fistfight. Bane, being physically stronger from his superhuman stuff, wins and unmasks Bruce, locks him in a heavily guarded cage (or in an official city prison, since he is a wanted man already) there in the city, and announces that Batman has been caught. (Alfred hides some Bruce's equipment from Bane's men who would be raiding Wayne manor to bring it to him later. Bruce creates a makeshift mask out of scraps of cloth.)

But the people of Gotham don't give in so easily, even under the threat of death. Because Bruce was right about them all along.

The citizens fight Bane's terrorist team.

Gordon (and co?) breaks Batman out (and other POWs?), since Gordon knows he's innocent (but not without drama from people who don't know, of course).

So Batman fights Bane so that Bane can't guard the bomb.

So Lucious Fox works on diffusing it.

Everything looks bright, until Marion Cotillard's character, Miranda, who had been helping Bruce up until now, is revealed to be an associate of Bane's (known as Red Claw) when she sabotages the good guys in some way (maybe she takes or blows up the Batwing, which they were going to use to take the bomb away from the city).

So then everything looks bleak, until Catwoman reveals to have had a change of heart (her motivation for resisting Bruce until then was out of hatred for his undeserved wealth, until she sees how much he's willing to sacrifice for others) and stops Red Claw in some way.

And thus, Batman beats up Bane (by damaging his super strength tech), while Lucious diffuses the bomb, while Gordon and the citizens beat Banes team. The city is saved.

Later, Batman and Gordon are alone, discussing the aftermath. Gordon is going to confess to the people about Batman's innocence, tell them about how much of a hero he really is. Maybe Gordon turns away for a moment, and he (as well as the audience) is expecting Batman to be gone when he turns back (as usual), but instead Batman's just slowly walking away into the morning sun, and responds to him.

The end.

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This story can work whether Batman's identity is revealed to the public or not. It's basically just a matter of whether you want the character to be over for good, or you want the Bale Batman to stay anonymous but be free from babysitting Gotham so he can join the Justice League in a later DC movie. I'm partial to the latter, since this trilogy would stand on it's own anyway regardless of what came after.

Bonus: If you want Joker in this movie, there's a perfect place for him without changing the overall story. Once Bane has established his new order, there's a new city system. Bane is king, his goons are police, and Scarecrow is judge, so what job is missing? I'll tell you what job. The job of 'Batman'. The Joker fills the role of new Batman, wearing the previous one's discarded mask, fighting both the citizens and Bane's men, mockingly imitating Christian Bale's Bat-voice, yelling nonsense about 'justice' and 'working in the shadows'. Then later, before the climax, the real Batman captures Joker Batman without too much trouble, since Joker isn't expecting him to come back and is thus caught off guard.