Well, perhaps in the fanfiction, the Joker has accidentally set off a chain of events that will destroy a part of Gotham he actually cares about (like an orphanage where he has some strange emotional connection). Batman, seeing the Joker's genuine distress, decides to save him so that they can work together to stop the disaster. Or it could be that the Joker has been framed for a crime he didn't commit (unlike his usual ones) by a powerful political figure, and Batman steps in to save him from being assassinated so that the truth can be uncovered.
One plot idea could be that the Joker is in a situation where he's being hunted by a more dangerous criminal group, and Batman, despite their long - standing enmity, saves him because he realizes the chaos that would ensue if the Joker fell into the wrong hands. Another could be that the Joker has some information vital to Gotham's safety, and Batman has to rescue him from a hostage situation to get that information. Maybe the Joker is poisoned, and Batman has to find an antidote and save him in order to also stop the spread of the poison throughout Gotham.
A possible plot is that the Joker gets kidnapped by a mad scientist who wants to experiment on his unique mind. Batman, knowing that the Joker's mind, as deranged as it is, is still a part of Gotham's complex ecosystem, decides to save him. Another idea is that the Joker is trapped in a collapsing building that was part of a trap set by another villain for both of them. Batman, being the hero he is, saves the Joker instead of leaving him to die, which then leads to a strange truce between them as they figure out how to deal with the other villain.
One idea could be that the villain has a change of heart after realizing Batman's true purpose in protecting Gotham. Maybe the villain has a personal experience that makes him see Batman in a new light. For example, his family is saved by Batman's actions indirectly, so he decides to return the favor when Batman is in a really tough situation.
One idea could be that Nightwing is captured by a powerful new villain in Gotham. Batman has to use all his detective skills to find Nightwing's location. Then, in a intense showdown, he battles the villain's minions and finally rescues Nightwing. Maybe Nightwing was being held in an abandoned warehouse on the outskirts of the city.
Well, perhaps Arrow is poisoned by a rare toxin that only Batman has the resources to find an antidote for. Batman races against time, using his network in the criminal underworld to track down the ingredients for the antidote. Meanwhile, he also has to fend off the villain's minions who are trying to stop him from saving Arrow. In the end, he manages to save Arrow just in the nick of time.
One plot idea could be that Superman is exposed to a new type of kryptonite that not only weakens him physically but also starts to affect his mind, making him a danger to himself and others. Batman, using his detective skills, discovers the source of this new kryptonite and figures out a way to neutralize it, thus saving Superman. Another could be that Superman is framed for a crime he didn't commit and is being hunted by the world. Batman, believing in his friend's innocence, uses his resources and stealth to clear Superman's name and save him from the wrath of the world.
One idea could be that Rachel, instead of being in a typical relationship with Batman, has a series of mind - games with the Joker. The Joker tries to use Rachel to get to Batman in a more psychological way, like trying to make her question Batman's methods. Another plot could be that Rachel discovers a hidden connection between Batman and the Joker from their past, which changes her perception of both of them.
In some fanfiction, the Female Joker might have a different origin story than the male one. For example, she could be a victim of a corrupt system who turns to chaos as a form of revenge. This could lead to an interesting dynamic with Batman, who is always fighting for justice in a more traditional sense. Batman may struggle with whether to help her or stop her, adding depth to their relationship in the story.
One idea could be that the deaged Joker, now with a child's body but his same devious mind, tries to manipulate the younger version of Batman into believing they are friends while secretly setting up traps. Another could be that the deaged Joker's actions cause Batman to re - evaluate his own origin story and how it might be related to this new, younger - but - still - dangerous foe. Or perhaps the deaged Joker forms an alliance with other deaged villains in Gotham, creating chaos that Batman has to stop.
One idea could be that Batman discovers a hidden weakness in an enemy that's about to destroy the Justice League. He uses his detective skills to find a way to counter it and saves them at the last minute. For example, if the enemy has a device that can nullify the League's powers, Batman figures out how to disable the device.
One plot idea could be that Harley Quinn is being hunted by a new super - villain in Gotham who wants to use her knowledge of the Joker's operations against him. Batman, despite their past differences, decides to save Harley because he realizes she could be a key in preventing a much larger threat to the city. He manages to rescue her from a dangerous trap set by the new villain and in the process, Harley starts to see Batman in a new light, not just as an enemy but as someone who actually cares about her well - being.
One interesting plot idea could be a fanfiction where the Joker somehow comes back to life in Arkham Knight. Maybe he was only in a coma and wakes up with a new, even more deranged plan to take over Gotham. He could start by manipulating the inmates in Arkham again, creating chaos from within the asylum.