The story would likely diverge from the original plot a great deal. Since Naruto is a prototype, there could be a new group of antagonists who are interested in his unique nature. His training would also be different, perhaps involving more scientific or experimental methods. His bond with his mentors like Jiraiya might be affected as they try to understand and guide this new 'prototype' Naruto. Also, the political situation in the ninja villages could change as other villages might see him as a threat or an opportunity due to his prototype status.
Well, his journey would be completely different. Instead of following the traditional ninja path, he'd be on a journey to understand and master his new naga abilities. His goals might shift from protecting the village in the normal way to perhaps protecting a new community of naga or finding a way to co - exist between humans and nagas.
Well, Naruto's personality would have an interesting transformation. He would likely become more of a risk - taker. The pirate world is full of uncertainties and dangers, and Naruto would embrace this. He might become more laid - back in some ways, enjoying the simple pleasures of life at sea like drinking grog (if they have something similar in this fanfiction world) and singing sea shanties. But at the same time, his competitive nature would still be there. He'd want to prove himself as a great pirate, perhaps competing with other well - known pirates. His naivete might also change a bit. While he was often naive in the ninja world, the harshness of the pirate life would make him more street - smart, yet still retain his positive outlook on life.
His relationship with Kurama might become more complex. Since he's now also a kitsune - like being. They could either become more competitive or find a new way to cooperate. With his friends, some might be in awe of his new form, while others might be a bit scared at first. But Naruto's kind heart would eventually make them all accept him as before.
If Naruto becomes cold - hearted, his relationships with the villagers would change drastically. The villagers, who once saw him as a hero, would now be faced with a cold and unapproachable Naruto. Children who used to look up to him would be scared. His friends from the Akatsuki days, like Nagato, might even see this new Naruto as a threat. Overall, his relationships would go from being warm and friendly to cold and distant, filled with suspicion and unease.
He'd become more responsible for the whole world perhaps. Since the Avatar has to keep balance everywhere.
If Naruto becomes a nukenin, his relationship with the village elders would be completely severed. They would see him as a threat, and he would see them as unjust. With his peers, some might side with him, believing in his innocence. Others would follow the village's orders out of loyalty. His bond with the Nine - Tails would also change. The Nine - Tails might offer more support, seeing Naruto as an outcast like itself.
His relationship with Sasuke would be greatly affected. Sasuke, who has his own experiences with the idea of killing, might see Naruto in a new light. They could either become rivals again or Sasuke might try to 'save' Naruto from his new dark path. With Sakura, she would be horrified. She's always seen Naruto as a positive force, and this change would make her question everything. She might even try to use her medical skills to 'cure' Naruto of his new - found killer tendencies.
If Naruto becomes a Saiyan in fanfiction, his relationship with his mentor, like Jiraiya, could be different. Jiraiya would have to guide Naruto in handling these new Saiyan powers. Naruto's friends might be both in awe and a little scared. For example, Sakura might be worried about Naruto losing control of his new powers. And his relationship with the villagers could change too. Some might see him as an even greater protector, while others might fear his new, more alien - like powers.
His abilities would become more lethal. Instead of using his Rasengan to just defeat opponents, he might use it to kill. His speed and stealth would be enhanced for more effective assassinations. His ability to gather information, like he did as a ninja, would be used in a more sinister way to track down his targets.
In a fanfiction where Naruto becomes Hokage early, the story would take a different turn. His early leadership could mean a faster implementation of his ideals. He might start projects to improve the living conditions of the common people in Konoha right away. However, he would also face opposition from the more traditionalist ninja who might think he's too young and inexperienced. His journey as Hokage would be a roller - coaster of learning, making mistakes, and growing into the role much earlier than expected.