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.
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.
Well, it could be that Naruto's relationship with the other Konoha ninjas changes drastically. They might see him as an outcast because of his association with Kisame. On the other hand, Naruto might try to bridge the gap between Konoha and the Akatsuki due to his upbringing by Kisame. This would create a whole new set of conflicts and alliances within the Naruto universe.
One possible plot twist could be that Naruto struggles to control the Sharingan at first. Since he's not from the Uchiha clan, the Sharingan's powers might act differently in him. For example, instead of the normal abilities like predicting movements, it might give him visions related to the Uchiha's past traumas. This could lead to Naruto having to deal with not only the power of the Sharingan but also the emotional baggage that comes with it.
Another plot twist might be that Naruto reads a future where the entire ninja world is in ruins. This could lead him to take extreme measures in the present to prevent that future from happening. He might try to unite all the ninja villages in a way that has never been done before, facing many obstacles along the way as different villages have their own interests and grudges.
One possible plot twist could be that Naruto develops a much darker and more ruthless side due to Zabuza's influence. Instead of the optimistic and friendly Naruto we know, he might be more solitary and calculating in his approach to battles and relationships. For example, he could be more willing to use underhanded tactics like Zabuza's use of hidden mist jutsu to ambush opponents.
One possible plot twist could be that Naruto inherits Hashirama's unique Wood Style jutsu much earlier and in a more powerful form. Since Hashirama was a master of this powerful ability, he might train Naruto intensively in it. This would make Naruto stand out even more in the ninja world and perhaps change the way his peers and enemies view him.
Maybe Naruto discovers some dark secrets about his family that completely shatter his positive outlook. For example, if he finds out that his father was involved in some unethical experiments. This revelation could send him into an emo state where he questions his identity and purpose.