Well, one possible plot twist could be that he turns out to be a long - lost relative of Bruce Wayne. Maybe he has some hidden knowledge about Wayne's family that changes the whole dynamic. For example, he could know about a secret inheritance or a past event that was covered up. Another twist could be that he's not who he seems at all, but rather an enemy in disguise, sent to infiltrate Batman's inner circle. He could start off as an ally, helping Batman with cases, but then gradually reveal his true motives which are to destroy Batman from within.
He could be a clone of Batman. Created by an unknown enemy, this clone could initially think he is the real Batman. As the fanfiction progresses, he starts to notice small differences in his memories or abilities. This discovery could lead to an identity crisis for him. And for Batman, it would be a race against time to find out who created the clone and why, while also dealing with the clone's actions which might be causing chaos in Gotham.
One possible alternate storyline could be that if he had come, he might have joined forces with Batman earlier to take on a new and more powerful villain. This could have led to a different dynamic in the Bat - family, perhaps changing the way Robin was trained or how Gotham was protected.
Maybe there's a magical accident that makes Hermione forget her relationship with Ron. In this state, the other guy has an opportunity to get closer to her. He could show her a different side of life or magic that she hadn't experienced with Ron. However, as Hermione starts to regain her memories, she has to make a choice between the familiarity and history she has with Ron and the new feelings she might have developed for the other guy.
One possible plot twist could be that Robin is influenced by a powerful and evil villain. Maybe the villain uses some kind of mind - control device or magic on Robin. For example, the Joker could find a way to make Robin see Batman as the enemy. Robin might then start attacking Batman and helping the Joker with his evil plans.
Well, perhaps in this fanfiction, Naruto is somehow transported to the Batman universe and is neglected by the local heroes at first. He then has to prove himself by using his ninja skills in Gotham's dark alleys, like using his shadow clones to confuse the bad guys and his speed to catch the elusive criminals.
It could be that there is some sort of misinformation spread by an evil organization. They create false evidence that Batman is planning to destroy Naruto's village. Naruto, being the protector of his village, decides to take pre - emptive action. He tracks Batman down and in a fierce battle, kills him. But then as he starts to investigate further, he discovers the truth and has to live with the guilt of killing an innocent (in this case, Batman who was misrepresented).
One possible plot could be that the Cheetah, who is usually a villain, has a change of heart. Maybe she gets injured during a fight with Batman and he shows her mercy. This act of kindness makes her see Batman in a new light, leading to a moment of unexpected attraction and the kiss.
Maybe a plot twist could be that they start to understand each other on a deeper level. Batman realizes how difficult it is for Catwoman to constantly be on the run from the law, and Catwoman sees the burden Batman carries to protect Gotham. This new - found understanding could change their relationship in the long run.
Maybe Harley Quinn's love for Batman causes her to turn against the Joker completely. This would be a huge shift as she has been so closely associated with the Joker for a long time. Her newfound love could lead her to try and reform herself to be worthy of Batman's love, and in the process, she might become an unexpected ally for Batman in his fight against Gotham's villains.
One possible plot twist could be that Catwoman is forced to work undercover for one of Batman's enemies to protect Batman, but Batman doesn't know. This would create a lot of tension between them as he tries to figure out why she seems to be acting strangely.
One possible plot twist could be that Poison Ivy decides to protect Batman's secret instead of using it against him. Maybe she realizes that Gotham needs Batman more than she needs revenge or chaos at that moment.