Well, one plot twist could be that Naruto's ability to solve the Millenium Puzzle unlocks a hidden power within him that's different from the Nine - Tails chakra. Maybe it gives him the power to time - travel, and he has to use this new power to prevent a great disaster in the ninja world that was foreseen by the ancient spirits connected to the Millenium Puzzle.
A possible plot twist is that the Millenium Puzzle actually contains the souls of ancient ninja warriors. When Naruto starts to solve it, these souls start to influence his mind and body. He has to fight against their negative influence while also using their knowledge and skills to defeat a new, powerful enemy that emerges in the Leaf Village.
Perhaps the Millenium Puzzle is a key to a secret dimension where all the most powerful and evil jutsu are stored. Naruto, by having it, is targeted by all the villains in the ninja world who want to get their hands on this powerful artifact. As he tries to protect it, he discovers that it also has the power to purify the most evil jutsu, and he uses this to his advantage to turn the tide against his enemies.
His relationship with Kakashi could also shift. Kakashi, being experienced, would be both intrigued and worried about Naruto having the Millenium Puzzle. He would try to guide Naruto in understanding and using it properly. Naruto would respect Kakashi's wisdom more in this scenario and would look to him for advice on how to handle the power and the responsibilities that come with the Millenium Puzzle.
One interesting idea could be a new magical creature introduced through the millenium puzzle. It might be a creature that holds the key to an ancient mystery in the Harry Potter world.
Often, Harry Potter himself is a main character. Since it's related to the Harry Potter universe, he is likely to be involved in the story centered around the millenium puzzle.
In a Naruto is Vergil fanfiction, it could be that Naruto's connection to Vergil is through a dream - like realm. Every time Naruto sleeps, he enters a world where he meets Vergil and learns from him. Over time, Naruto starts to incorporate Vergil's values into his own. He becomes more focused on power for the sake of protecting those he loves in a more 'Vergil - esque' way, which means he might be willing to make some sacrifices that he wouldn't have considered before, like sacrificing some of his own personal relationships for the greater good of the village.
Well, it could be about a girl who gets trapped in a world full of puzzles. Maybe she has to solve various puzzles to find her way out or to uncover some secrets. For example, she might start in a mysterious maze - like place where each turn presents a new riddle or brain - teaser. As she solves the puzzles, she could meet strange characters who either help or hinder her progress.
A possible plot twist is that Naruto is actually a reincarnation of a great Jedi. He starts having strange dreams and visions of a past life as a Jedi, and these memories gradually influence his actions as a ninja. His friends might be confused or even a bit scared at first, but as he learns to control this new side of himself, they come to accept and rely on his Jedi - inspired skills in their battles against stronger foes.
One possible plot twist could be that Naruto, after becoming a Madara fan, starts to question the traditional values of Konoha. He might see Madara's vision of a more unified world under his rule as something appealing. This could lead to a rift between him and his friends as they struggle to understand his new perspective.
In this fanfiction, Naruto might look into the future and find out that the new generation of ninjas has lost their way. They no longer value the things he fought for, like friendship and hard work. So, he has to come up with a plan to inspire them again. He could start by sharing his own experiences and showing them the importance of the ninja way.
One possible plot twist could be that Naruto's Sharingan has unique abilities not seen in the regular Uchiha Sharingan. Maybe it can combine with his Sage Mode in unexpected ways, like seeing chakra flows more clearly even in Sage Mode, enhancing his combat skills.
One possible plot twist could be that Konan discovers a hidden power within Naruto that he's not even aware of himself. This newfound power could attract the wrong kind of attention from other ninja villages or even from some secret organization. Another twist could be that Konan's past catches up with her in a way that endangers their marriage. Maybe an old enemy resurfaces and tries to use Konan to get to Naruto. Or perhaps there's a prophecy that says their union will bring either great destruction or great peace, and they have to figure out which it will be.