Well, a plot twist could be that the modern army's weapons are actually ineffective against the fantasy creatures because they are made of some sort of magical substance that absorbs or deflects the bullets and missiles. Then, a lone scientist in the modern army discovers a way to combine magic and technology, creating a new weapon that can defeat the fantasy side. Another plot twist could be that the fantasy side has a prophecy that a group of modern soldiers will save their world, so instead of fighting, they welcome the modern army and ask for their help against an even greater evil within their own realm.
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.
One possible plot twist could be that Hinata discovers a new power within herself during the fight against Pain. Maybe she can tap into some ancient Hyuga ability that even she didn't know existed. This new power could turn the tide of the battle and surprise both Naruto and Pain.
One exciting plot twist could be that Venom actually has a change of heart. Maybe he realizes that he and Spider - Man are both victims in a way, and they end up teaming up against a bigger threat. Another could be that Spider - Man gets infected by a different symbiote that makes him even more powerful, but also more unpredictable, and now Venom has to decide if he wants to fight this new version of Spider - Man or join him.
One interesting plot twist could be that Neji discovers a new power within his Byakugan that makes him evenly matched with Naruto's Nine - Tails power. Maybe he unlocks a hidden ability that allows him to see through Naruto's chakra cloaks or disrupt the Nine - Tails' chakra flow. Another plot twist could be that Naruto loses his access to the Nine - Tails' chakra during the fight, and has to rely solely on his own skills and training, making it a much more even match against Neji.
One interesting plot twist could be that Goku and Beerus end up teaming up instead of fighting. Maybe they discover a common enemy that is even more powerful than them. Another could be that Beerus loses his power temporarily and Goku has to protect him from other villains while also trying to figure out how to return Beerus' power.
Maybe in the fanfiction, Naruto loses his chakra early on in the fight against Pain. But then he discovers a hidden power within himself that is not related to chakra, like a spiritual power from his Uzumaki heritage, which he uses to turn the tables on Pain.
A great plot twist could be that the monster turns out to be the girl's long - lost brother who was experimented on and turned into a monster. This would completely change the dynamic of their fight as she now has to find a way to save him instead of just defeating him.
In the fanfic, Naruto might destroy the army in a very unique way. Instead of using his typical Rasengan or Shadow Clone Jutsu, he could discover a new power within himself. Maybe he unlocks a special form of Sage Mode that gives him the ability to control the elements in a completely different way, allowing him to take on the army with ease.
Well, one plot twist could be that the triplets have some sort of unique magical ability that no one has ever seen before. Maybe they can communicate telepathically with magical creatures, which could lead to all sorts of adventures and trouble as they try to understand and control this power.
A really interesting twist could be that Hermione's presence in Middle - earth is actually a key part of an ancient prophecy that no one knew about. As Aragorn's sister, she might be the one to unlock some great power or knowledge that is crucial for the victory over evil. This would make her a central figure in the story, not just as Aragorn's sister but as a key player in the fate of Middle - earth.