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.
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 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.
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.
One possible plot could be that Harry, using his magic skills, protects Naruto from the various threats in the Naruto universe. For example, he could use spells to shield Naruto from enemy ninjas' attacks. He might also use his knowledge of magic to help Naruto understand some concepts that are difficult in the ninja world, like a different way of looking at chakra manipulation which could be related to how magic works in Harry's world.
Well, in such a fanfiction, Naruto might take over Konoha to reform it. Maybe he's tired of the old ways and wants to make it more inclusive and fair for all ninjas, regardless of their background.
One possibility is that Minato takes Naruto away to a secret training ground. There, he could start to teach Naruto advanced jutsu that he never got to pass on before. This would be a way for Minato to make up for lost time and help Naruto become even stronger.
Well, one possibility could be that Kushina takes Naruto away to protect him from the dangerous world of shinobi. Maybe she wants to raise him in a peaceful place away from the constant threats and battles in the Hidden Leaf Village.
One plot twist could be that the princess is actually a spy. She was planted to be 'captured' so that Naruto would come to save her and lead the rescuers into a trap. But Naruto, being observant, notices some small details that give her away and he has to turn against her to save himself and his comrades.