I think that the animated adaptation of Alan Moore & Dave Gibbon’s Batman: The Killing Joke (a comic book story roughly twice as long as a regular comic) was a decent effort but lacked the emotional punch it should have. Here’s how I would have done the story in animated form. Spoilers to both versions of the story of course.
The animated version has the right idea by having more scenes in the beginning with Barbara Gordon as Batgirl, so that what the Joker does to her has more of an emotional impact. However, by having that section completely disconnected from the rest of the movie, it mutes the impact. Plus, since this is a Joker story, the viewer gets a bit impatient waiting for the Joker to show up. But by the time he does the viewer has gotten invested enough in Batgirl’s story, told from her perspective that when the story that’s supported to be adapted finally turns up, it actually derails the movie that we’d been watching to this point. So to connect the stories more fully I’d do the following:
I’d establish that the Joker is so skilled at escaping that he more or less chooses when he leaves Arkham Asylum. The initial sequence would therefore also be a clash with the Joker, only involving Batgirl as well. As Batman and Batgirl tracked the Joker down, Batman would admit that despite having allies, he still tended to feel isolated and alone during his war on crime. Whenever he and Batgirl were alone, he’s noticeably let his guard down in his facial expressions, only to resume the stony face book whenever others were present. Also, Batgirl would observe that Batman keeps trying to put the Joker away and the Joker keeps escaping, and that the two of them were on a broken record. Meanwhile her father, Commissioner James Gordon would get into a debate with Batgirl as to whether or not the Joker was born evil (I think it works regardless of whether Gordon knows Batgirl is his daughter for this to work, but it might work better if it does, for reasons that will become apparent below).
Eventually Batman and Batgirl would capture the Joker. By this point Batgirl and her father’s debate would spill into the Joker overhearing them argue. The Joker would be motivated to not only escape sooner than usual but also try to drive Gordon mad to prove his evil was the result of a bad day and not his basic nature. Not realizing that the Joker had escaped, Batgirl, wanting to prove her own point, and stressing that the two of them were likely to get each other killed, would convince Batman to visit the Joker in Arkham. From there we’d head to the story of the comic version of the story with Batman learning of the Joker’s escape.
After the Joker killed the guy at the carnival he would remark that Batgirl was the only decent one among the do-gooders, thus emphasizing that he doesn’t know Batgirl is Barbara Gordon. This would have created further pathos when he shot and stripped Barbara and captured her father to try to drive James Gordon mad for what he said before.
The next bit would follow pretty closely the original story, with Joker remembering one possible version of his past as he subjects a stripped James Gordon to a mad carnival ride. He’d taunt Gordon with delight at watching the man who insulted him get dragged down by a bad day, just as he was, or at least how he remembers it that day.
When Batman was alone with Barbara, his face would soften and show his anguish, and he would promise to Barbara to really hurt the Joker for what he did to her. But Barbara would tell him no, because that way the Joker wins, by dragging them to his level. She’d tell him to try to redeem him one more time. Batman, touched by Barbara’s strength after the trauma she’d experienced, would promise to honour her wishes.
This promise would be strengthened further by him finding James Gordon, having survived the attempt by the Joker to drive him mad and having him tell Batman to do this by the book. Armed by the strength shown by both Gordons, he’d be able to first keep his cool and defeat the Joker, and then, at a point when he really just wants to hurt the Joker, offer to end their conflict just this once. The Joker would decline and tell his joke about being alone. Batman would laugh, but a bit uncertainly.
I’d end the story with Batman taking James to Barbara after James had been patched up. Batman would start to leave only to be asked to stay by his friends. Batman would think about how his friends, despite their trauma would heal and welcome him in their world, while the Joker was alone. Batman would finally realize that with such strong friends he could never be alone, so the Joker’s joke about being alone was no longer as funny. Having thus decided this, he’d realize that despite what they’d endured, this time the joke was on the Joker. The final shot would be of the Joker in Arkham, now completely broken with no energy to attempt an escape.