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.
A really interesting plot twist can be found in 'Batman and Hulk: Switching Sides'. Here, due to some sort of magic or science gone wrong, Batman starts to show Hulk - like rage and the Hulk becomes more calculating like Batman. This completely changes their dynamic and how they interact with the villains in the story.
There's a fanfiction titled 'The Hidden Agenda'. The plot twist is that the Joker has somehow managed to manipulate events to make Batman and Hulk fight each other. But as the story unfolds, it's revealed that the Joker has an even more sinister plan that involves using their fight for his own gain. It's a great twist that keeps you on your toes as you read.
In some Batman vs Avengers fanfiction, a great plot twist is when Batman manages to hack into the Avengers' communication system and makes them fight among themselves. He then uses the chaos to his advantage. Another cool twist is that there's a greater threat looming, and Batman and the Avengers have to put aside their differences and work together. But as they do, they discover that one of the Avengers has been replaced by a shape - shifter, and Batman has to figure out who it is before it's too late. There could also be a plot twist where Batman uses a device that actually amplifies his own strength and skills to the point where he can match the Avengers' superpowers, at least temporarily.
A really cool plot twist would be if Batman manages to steal all of Thanos' Infinity Stones and use them against him. This would completely turn the tables. Or perhaps there's a plot twist where Batman uses his detective skills to uncover a secret weakness of Thanos that no one else knew about. Maybe it has something to do with Thanos' past or his family, and Batman uses this knowledge to his advantage in the fight.
A really interesting plot twist could be that the villains from both universes are actually being controlled by a single, greater evil. For example, Queen Beryl and the Joker are being manipulated by an interdimensional being. This would force Sailor Moon and Batman to put aside their differences in fighting styles and beliefs to take on this new threat.
A really interesting plot twist could be that the Grimm from RWBY are somehow connected to the madness in Arkham Asylum. Maybe they are being summoned by one of the inmates who has some sort of dark magic. Another plot twist could be that a character from RWBY, like Yang, turns out to be related to one of the Arkham Asylum staff in a very unexpected way.
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.
One possible plot twist could be that Pennywise actually has a fear of bats, which gives Batman an unexpected advantage. Another could be that Pennywise manages to possess Batman and uses his skills and resources to wreak havoc in Gotham, but Batman's consciousness fights back from within. Or perhaps there's a plot twist where the two form an unlikely alliance to fight a greater evil that is threatening both their existences.
In some 'naruto batman fanfic', a plot twist could be that Naruto's chakra is somehow linked to the power source of Batman's technology. So when Naruto is in danger, it affects Batman's gadgets. This unexpected connection changes the way they fight together and adds a new layer of complexity to their relationship.
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.
Well, a great plot twist could be that Batman discovers that Naruto is being controlled by an evil force. Instead of fighting Naruto, he decides to help him break free from the control. This would lead to an unexpected alliance between them. Another plot twist could be that the fight between them is actually a test set up by some higher - level beings from both universes. They are being watched and judged based on how they fight and interact. And if they pass the test, they are given a special power or mission. Or maybe there's a plot twist where Naruto's friends from Konoha are kidnapped and held hostage by someone who wants Batman to defeat Naruto. Naruto then has to decide whether to fight Batman or try to find another way to save his friends in this fanfic scenario.
In some fanfictions, the plot twist could be that it was all a simulation or a dream within a dream. Batman thinks he has killed Superman, but then realizes it was all a false reality created by some powerful entity. Or perhaps the twist is that Superman's death at Batman's hands is a necessary sacrifice to save the multiverse. Superman willingly allows Batman to kill him to prevent a greater evil from spreading across different universes.