A great plot twist could be the discovery that Naruto and Raven are related in some way through a long - lost multiversal connection. This would completely change their dynamic and the way they interact with each other. Also, perhaps Naruto's ability to transform into different forms gives Raven new insights into her own powers of transformation or shape - shifting. Another plot twist might be that a powerful artifact in the DC New 52 world is actually linked to Naruto's world, and only they can unlock its true potential together, leading to a race against other characters who want to use it for evil purposes.
A really unique plot twist in DC Vampire fanfiction can be that the Green Lantern Corps has to deal with a vampire - like entity that feeds on the energy of their rings. This forces them to find new ways to power their rings and fight this entity. And sometimes, a plot twist is that a vampire version of Aquaman rules the underwater world, and the normal Aquaman has to figure out how to stop him without getting turned into a vampire himself.
Well, a great plot twist might be if the Sharingan had a unique effect in the SAO world. For example, it could allow the user to see hidden codes or glitches in the game. And what if some of the SAO bosses were actually jinchuriki - like beings? Naruto would have to use his knowledge of taming the nine - tails to deal with them. Also, if Asuna had some sort of hidden ninja bloodline ability that gets awakened when she meets Naruto, that would be a really cool twist.
Naruto has the ability to create shadow clones. These clones could be used in combination with Raven's empathic powers. The clones could spread out and gather information about the emotions of enemies in different areas, and Raven could then use this information to strategize better. Also, Naruto's Rasengan, a powerful chakra - based attack, could be infused with Raven's Azarathian magic to create a new, even more destructive attack that has elements of both their powers.
One interesting plot twist could be when a Splatoon character suddenly gains Naruto - like powers. Imagine an Inkling being able to use the Rasengan. It completely changes the dynamic of the story.
A really interesting plot twist can be when the characters from Undertale end up in the Naruto world and they have to adapt to the ninja way. For example, Sans using his shortcuts in the middle of a ninja battle, which throws everyone off guard. It's unexpected and adds a whole new level of humor and chaos to the story.
In some fanfictions, a big plot twist is when Naruto suddenly gains a Devil Fruit ability, completely changing the power dynamics. For example, in 'Naruto's Devil Fruit Adventure', he gets a powerful fruit that makes his ninja skills even more formidable.
One really cool plot twist is when the values of the Naruto universe start to influence the Decepticons in unexpected ways. For example, the concept of friendship and loyalty that Naruto and his friends uphold might start to make some Decepticons question their own motives and allegiances, which leads to a whole new set of conflicts and resolutions in the fanfiction story. This not only adds depth to the story but also makes for a very engaging read as it challenges the typical Decepticon - like behavior we are used to in the original Transformers franchise.
Perhaps a plot twist where an evil force is manipulating both their universes and they are the only ones who can see the signs. Naruto and Caulifla must put aside their differences and combine their powers in a way no one thought possible to stop this greater evil that threatens both their worlds and the fabric of reality itself.
Another interesting plot twist is when the main villain in the Naruto world turns out to be in cahoots with an evil Bakugan from another dimension. This forces Naruto to not only fight his regular enemies but also understand the complex politics and power struggles in the Bakugan world to stop the greater threat. It's a really cool way to merge the two universes.
In some fanfictions, like 'The Secret Alliance', there's a plot twist where Naruto and Kenichi form an unexpected alliance against a common enemy that was thought to be an ally. It completely changes the dynamic of the story.