The ending turns Batman from a solo act into the head of a family, and in my opinion that is the smartest thing the film does with a character who has been brooding for decades.
Gotham is saved when the heroes, citizens and even some villains work together to hold the city's broken pieces in place. The picture is literal: bricks and people holding a city together. Batman accepts that he needs other people and treats Alfred, Robin and Barbara as his family. He tells Robin who he really is, which in a Batman film is the sign of real trust.
The warden of the Phantom Zone allows Batman to remain in Gotham as its hero. Batman gives the escaped villains a head start before he goes after them, which sets up more adventures for the new team.
Why does it work? It could be argued that the Joker's whole plan tests one weakness, and he is right about it. Batman spends the film insisting he does not need a rival, a sidekick or a commissioner, while the Joker only wants to be acknowledged. The Joker even lets himself be caught and the villains surrender, because he knows that taking away Batman's enemies leaves him with nothing to fight and nobody to talk to. Perhaps that is the sharpest joke in the script: the hero who claims to be alone is the one who needs a rival most.
How does that compare with the rest of the series? In Batman (1989), directed by Tim Burton, Jack Nicholson's Joker is a mirror to Batman's trauma, and in The Dark Knight, directed by Christopher Nolan, he is a force of chaos. Here the answer is gentler and, perhaps, more useful: the way to beat the Joker is to stop pretending you are alone. The adoption of Dick Grayson also reads differently from Batman Forever, where Robin arrives after Two-Face destroys a circus family, and from Batman & Robin, where the partnership is strained and Alfred's niece Barbara is pulled into the heroes' world. Here the family is chosen, by accident first and then on purpose. The fear Batman admits, of losing people again, also echoes Batman: Mask of the Phantasm, where flashbacks show how close Bruce came to giving up his crusade for a normal life with Andrea Beaumont.
The craft backs up the theme. Animal Logic gave the film an emulated stop motion look, with a jitter algorithm that leaves small gaps and crooked placement between bricks, and generated 81,854 textures such as scratches and fingerprints. That imperfection matters at the finish: a city held together by crooked, handled toy bricks feels more human than a polished one. Chris McKay directed with that tone in mind, and I would argue it is why the closing image lands as sincere rather than only funny.
