A really cool plot twist could be that Naruto is resurrected in the body of another character. He would have to adapt to this new form and also convince his friends that he is really Naruto. This would create a lot of interesting situations, like when he tries to use his old techniques in the new body and discovers that they work differently.
Maybe Naruto is resurrected by an unexpected force, like an ancient and forgotten jutsu that was thought to be lost. This could lead to a whole new arc where he has to figure out who resurrected him and why, while also dealing with the fact that the world has changed since his death.
One possible plot twist could be that Naruto's parents, Minato and Kushina, are resurrected but they have lost their memories. This would create a whole new dynamic as Naruto has to help them regain their past while also dealing with his own emotions of having them back. Another twist could be that their resurrection is part of a larger, darker scheme by an old enemy who wants to use them against Naruto. For example, the enemy might be able to control them to some extent and make them fight Naruto, which would be a heart - wrenching situation for Naruto as he has to face his beloved parents in combat.
One interesting plot twist could be that the animals teach Naruto unique jutsu that are based on their natural abilities. For example, the birds could teach him a flying jutsu that no human has ever mastered before. Another twist might be that Naruto discovers he can communicate with all animals, not just the ones that raised him, which gives him an edge in battles and in gathering intelligence.
Maybe the Akatsuki members who kidnapped Naruto start to have second thoughts. Some of them might realize that Naruto is not just a tool for their goals. They could begin to see his value as a person and his potential to bring peace in a different way. This could lead to internal conflicts within the Akatsuki group.
Well, a plot twist might be that Naruto's resurrection is part of a grander scheme by an old enemy. This enemy brought him back not out of kindness but to use him as a weapon. Naruto, being Naruto, would then have to fight against this control while also dealing with the changes in the ninja world since his death.
One interesting plot twist could be that their resurrection is part of a grand scheme by an ancient magic user who wants to use their combined power for some dark purpose. But James and Lily, being the good people they are, resist and try to turn the tables on the evil plotter.
Well, perhaps Naruto is brought back to Konoha not as himself but in a transformed state. He could be in a form that combines his own chakra with some ancient and mysterious power. This new form might make his friends initially not recognize him, leading to some tense and emotional moments. Also, it could be that his return is part of a larger prophecy that the village was unaware of, and his presence now sets in motion a series of events that will either save or doom Konoha.
One possible plot twist could be that the kidnappers turn out to be working for an old enemy of the Hidden Leaf who has a personal vendetta against Naruto. Maybe they plan to use Naruto as a sacrifice to revive an ancient evil. Another twist could be that the kidnappers are actually being controlled by a powerful genjutsu user within the village who wants to disrupt the sealing for their own political gain.
One possible plot twist could be that Anko's unorthodox training methods lead Naruto to develop a unique fighting style early on. For example, he might learn some of Anko's snake - related jutsu and combine them with his own shadow clone technique in unexpected ways. This could make him stand out even more among his peers and draw both admiration and envy.
Well, a really interesting plot twist could be related to Naruto's eyes. In the normal Naruto story, he has blue eyes. But if he's raised by the Hyuga, there could be some strange phenomenon with his eyes. Maybe he starts to show some Hyuga - like traits in his eyes, not exactly the Byakugan, but something in between. This could lead to him being both feared and respected in the ninja world. And also, his role in the Hyuga clan's internal politics could be a major plot point. For example, he might be used as a pawn by some and a savior by others.
Maybe he gets to relive his childhood but with a different mentor. Instead of Iruka, he could be mentored by someone like Kakashi right from the start. This would change his training methods and the way he approaches learning ninja skills. It could also lead to different relationships with his classmates as Kakashi might push him in different directions.