One possible plot twist could be that the new Naruto has different abilities. Maybe he has a unique form of chakra control that the original Naruto didn't have. This could lead to different battle strategies and interactions with other characters. For example, in a fight against Sasuke, he might use his new chakra control to create unexpected jutsus.
The new Naruto could also have a different personality. Instead of being the head - strong and determined Naruto we know, he could be more calculating and sly. This would change his relationships. His friends might be initially suspicious of him, and he'd have to work hard to earn their trust.
Perhaps the new Naruto is from an alternate timeline. He might bring knowledge of future events or different ways of doing things in the ninja world. This could disrupt the existing order and cause chaos as some characters might try to use his knowledge for their own gain, while others would be wary of it.
Well, one possibility is that the 'new' Naruto, who is actually the original Naruto in a different role, could change the course of events in the Hidden Leaf Village. Maybe he would approach missions and training in a completely new way, leading to different power-ups and relationships with his comrades.
One possible plot twist could be that in the other dimension, Naruto finds out that all his friends have different personalities. For example, Sasuke could be a peaceful scholar instead of a brooding avenger. Another twist might be that the chakra system works completely differently in this new dimension. Maybe instead of using hand signs, they use some kind of mental power to perform jutsus. Also, Naruto could discover that the Akatsuki in this dimension are actually the good guys, fighting against an evil ninja clan that wants to take over the world.
One possible outcome is that Naruto, being in Itachi's place, might have a very different approach to dealing with the Uchiha clan situation. Naruto is known for his strong belief in redemption and friendship. He could have tried to reason with the Uchiha clan instead of the events that Itachi had to go through. This might have led to a different relationship between the Uchiha and the village.
In this type of fanfiction, the plot might develop in a way that Naruto tries to fix things he previously thought were okay. For instance, he could decide to reform the ninja academy's training system. He has the experience of being a student there, so he knows the flaws. This would then lead to him facing opposition from the traditionalists in the village, creating a lot of conflict and drama in the story.
One possible plot twist could be that Fem Itachi has a hidden agenda in taking Naruto to the Akatsuki. Maybe she's actually trying to protect Naruto from a greater threat by pretending to bring him to the Akatsuki. Another could be that Naruto discovers a long - lost connection between his family and the Akatsuki through this journey, which changes his perspective on the whole situation.
Sakura would be greatly affected. If the new Naruto is different, she might have a hard time adjusting. She was used to the old Naruto's clumsy but sincere attempts at flirting and his unwavering loyalty. A new Naruto could make her question her feelings and role in the group.
In such a fanfic, Naruto might have to carry out Itachi's mission to protect Konoha in a different way. He may use his own unique ninja skills and positive attitude to face the Akatsuki. For example, instead of using Itachi's Sharingan techniques, he would rely on his Shadow Clone Jutsu and Rasengan variations.
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, perhaps in the fanfiction, Naruto being Kurenai's sensei could lead to him teaching her some unorthodox methods. Since Naruto has his own way of doing things, he might introduce her to new ways of fighting or thinking that completely revolutionize her ninja skills. This could create interesting storylines where Kurenai has to adapt to Naruto's teaching style while still holding on to her own values.
One possible plot twist could be that Naruto discovers a secret conspiracy against Hinata's family while being her bodyguard. Maybe the real threat is not from an obvious enemy but from within the village's own political circles. He then has to protect Hinata not just from physical harm but also from being used as a pawn in this political game.