Another cool plot twist might be that the Supreme Deity turns out to have an ulterior motive for interacting with Naruto. Instead of being a purely benevolent figure, there could be a darker plan at play, like using Naruto to gain power over the ninja world. This would put Naruto in a very difficult position, having to decide whether to trust the deity or not.
Well, perhaps a really cool plot twist is that Naruto and Shizune time travel to a future version of the ninja world that is on the verge of destruction. They then have to figure out what went wrong in their own time to cause this and find a way to prevent it from happening. Or, they could travel back to a time when Orochimaru was still a good guy, but their presence somehow starts to corrupt him, leading to a whole new set of problems. Another idea is that they time travel and end up in the body of other characters, which is really strange and they have to adapt to these new identities while also trying to find a way back to their normal selves and their own time.
One interesting plot twist could be that Naruto starts to have memories of Tobirama's past battles. This would make him question his own identity and purpose. Another could be that Tobirama's reincarnation in Naruto causes a shift in the power dynamics among the villages. It might make other villages see Konoha as a greater threat or as a source of new knowledge.
One of the most interesting plot twists could be that Naruto discovers a new form of chakra that has the power to rewrite history. This would completely change the power dynamics in the Naruto universe.
One interesting plot twist is that the chakra seal on Naruto is actually a key to an ancient power source. At first, it seems like a hindrance, but as the story progresses, it's revealed that the seal was placed there to protect this power until Naruto was ready. This flips the whole concept of the chakra seal from a negative to a positive in an unexpected way. Also, there could be a plot twist where the sealing of Naruto's chakra was a misdirect, and it was actually someone else's chakra that was being targeted, and Naruto was just a decoy.
Well, a great plot twist could be that the enemies of the village learn about Naruto being Minato's reincarnation and try to use it against him. They might try to manipulate his new - found connection to Minato in some way, like using it to create doubts in Naruto's mind about his own identity. Another could be that as Naruto is the reincarnation, he has access to some of Minato's special chakra that has unique properties. This chakra could react in unexpected ways when combined with Naruto's own, leading to new powers and abilities that no one anticipated.
A possible plot twist is that Naruto, reborn as Itachi, uses his knowledge of future events to change the Uchiha clan's fate. He could try to expose the real masterminds behind the planned Uchiha coup and prevent the massacre. This would completely change the course of the story, not just for the Uchiha but for the entire ninja world. Also, his relationship with other characters like Kakashi would be very different. Kakashi, who had a certain view of Itachi, would now be dealing with a Naruto - influenced Itachi.
One interesting plot twist could be Naruto accidentally changing the reality of the shinobi world into a utopia where there is no war, but then realizing that the lack of conflict has made the ninja lose their edge. Another could be that Naruto's reality - controlling power is actually a curse from an ancient being, and he has to find a way to break it. And perhaps, Naruto changes reality in a way that makes all his friends forget who he is, leading to a journey of self - discovery for him to make them remember.
One possible plot twist could be that the Fem Kyuubi has some hidden Halo powers that are awakened during a crucial battle in the Naruto universe. This could change the dynamics of the fight and her relationship with Naruto. Another might be that characters from the Halo universe are somehow transported to the Naruto world, leading to some really interesting cultural clashes and power struggles.
A possible plot twist could be that Robin's transformation into Red X is part of a larger plan by a villain. The villain wants to use Robin as Red X to create chaos in the city. But Robin, while in the Red X form, starts to understand the criminal underworld better. He uses this knowledge not only to clear his name when his friends suspect him but also to turn the tables on the villain by using the Red X powers in unexpected ways.
One of the most interesting plot twists could be the sharing of powers. For example, Naruto's ability to use chakra might combine with the unique demonic powers in Highschool DxD in unexpected ways. Maybe a character from Naruto's world gains a devil fruit - like ability from the Highschool DxD universe. Another could be a character from Highschool DxD learning how to use ninjutsu, which would completely change the power dynamics in their own world.