Another plot idea could be that the looking glass is a portal to different versions of Gotham City. Batman and Joker are constantly shunted between these versions. In some, they are friends, in others they are mortal enemies with even more extreme versions of their personalities. They have to figure out the rules of this looking - glass world to stop it from collapsing all the versions of Gotham together.
Their relationship would become very different. In the normal Gotham, they are arch - enemies. But through the looking glass, they might become reluctant allies. The Joker might start to see Batman in a new light, and Batman might understand the Joker's motives a bit more. For example, if the looking - glass world has different moral standards, the Joker's actions could seem more justifiable to Batman, at least in that context.
Alice could get stuck in a time loop in the looking - glass world. Every time she tries to break free, she ends up at the beginning of a particular day in the looking - glass world. This could lead to her repeating conversations with characters like the Mad Hatter and learning new things about them each time.
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.
One idea could be that Alice discovers a hidden realm within the looking - glass world where all the characters' personalities are reversed. For example, the usually kind White Queen is now a bit cruel. Another could be that Alice has the power to change the rules of the looking - glass world, like making time run backwards. Or perhaps she teams up with the Jabberwocky to overthrow an unjust ruler in that strange world.
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 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.
Some fanfictions might focus on the psychological aspects of their relationship. The Joker's insanity and Batman's unwavering sense of justice create a really unique dynamic. In slash fanfiction, this could be explored in terms of how they understand each other on a deeper level, perhaps a level that no one else can fathom.
One idea could be exploring a world where Batman and Joker have to team up against a greater evil. Maybe a powerful alien force arrives in Gotham and they realize they need to combine their skills, even if reluctantly.