In a fanfiction where Naruto becomes a nukenin, it could be due to a prophecy that the village misinterprets. The village elders think Naruto will bring destruction, so they try to imprison or kill him. Naruto, not wanting to be a victim, escapes and becomes a nukenin. He then travels around, learning new jutsu from other lands and becoming stronger. Eventually, he might come back to the village to show them that their fears were unfounded, but by that time, he has become a very different ninja, with a new set of values and powers.
Perhaps Naruto becomes a nukenin in order to protect a secret that could endanger the village if it were to be exposed. He leaves the village to keep this secret away from those who might misuse it. In his journey as a nukenin, he could develop new jutsu in isolation, away from the constraints of the village's training methods.
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.
With his friends in Konoha, like Sakura and Kakashi, there would be a major shift. Sakura might initially be conflicted between her loyalty to the village and her friendship with Naruto. Kakashi, being a more experienced shinobi, might understand Naruto's reasons better but still be bound by his duties to the village. Overall, Naruto's departure as a nukenin would create a lot of emotional turmoil among his relationships.
One idea could be exploring the backstories of the nukenin in more detail. Maybe they had noble reasons for leaving their villages that were misinterpreted.
Sasuke is often a popular character in 'nukenin naruto fanfic'. His complex backstory and his time as a sort of nukenin - like figure make him a prime candidate for such stories.
Well, in some 'nukenin naruto fanfic' stories, the missing - nin could form their own small group. This group might not be entirely evil but rather just trying to survive in a world that has shunned them. They could have unique abilities and codes that they follow, which make for an exciting read.
Add depth to the plot. Instead of a simple story of good vs bad nukenin, explore moral grey areas. Maybe the villages aren't always in the right when they label someone as a nukenin. And show how the nukenin deal with the consequences of their status in a complex way.
One possibility could be that Naruto is drawn to boxing because of its physicality and the determination it requires. He might see it as a new way to test his strength and endurance outside of ninja battles. Maybe he starts training with a local boxing coach who sees his potential and helps him develop his skills.
One possibility is that Naruto, with his determination, could adapt Zeref's powers in a unique way. Maybe he'd use Zeref - like magic to enhance his ninjutsu. For example, he could infuse Zeref's death - based magic into his Rasengan, creating a more powerful and dangerous attack. Another aspect could be Naruto's personality change. If he becomes influenced by Zeref, he might become more brooding and less of the cheerful ninja we know. However, his core values of friendship and protecting the village would still likely be there, just warped a bit by Zeref's dark nature.