A really cool plot twist might be if the Joker and Batman swap personalities or at least aspects of their personalities. The Joker could suddenly start fighting crime in a very un - Joker - like way, while Batman starts to act more erratically. This could be due to some sort of magic or advanced technology gone wrong in Gotham, and the city has to deal with this strange new situation.
In some fanfictions, a plot twist could be that Batman discovers the Joker has a family or a past that explains his madness in a more sympathetic way. For example, if it's revealed that the Joker was once an ordinary man who was experimented on by a corrupt organization, and Batman has to decide whether to still see him as a pure villain or something more complex. This could change the way they interact in the story.
One interesting story could be where Joker tries to turn Gotham against Batman in a very psychological way in the fanfiction. He spreads rumors and false evidence to make the citizens doubt Batman's motives.
Perhaps in the fanfiction, Batman is revealed when a new technology is used against him. Let's say a villain creates a device that can see through disguises and Batman's high - tech cowl is no match for it. This would completely change the dynamic in Gotham as all his enemies would know who he is.
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 interesting story could be where Joker captures Batman and tries to break his spirit by showing him a distorted Gotham City that he has created in an abandoned area. Joker might use his henchmen to taunt Batman while he's trapped, but Batman uses his wits to find a way out and turn the situation around on Joker.
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.
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.
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.
Well, sometimes in such fanfiction, there are alternate universes. For example, a world where the Joker and Batman have to team up against a greater evil. This flips their typical dynamic on its head and makes for an exciting read.
In some fanfictions, like 'The Unlikely Alliance', the plot twist is that the Hulk is actually being controlled by an unknown villain who wants to use him to take down Batman. Batman has to figure out not only how to stop the Hulk but also who is behind it all.