It could be that Naruto is forced to become a nukenin due to a power struggle within the village. Some corrupt elements in the village want him out of the picture because of his growing influence. As a nukenin, he starts to build his own network of friends and comrades who believe in his cause and together they strive to bring about a change in the shinobi world that is more just and inclusive.
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.
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.
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.
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.
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.
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.
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.
Maybe the plot could revolve around Naruto getting influenced by a powerful and evil entity. This entity could corrupt his mind, making him believe that the only way to achieve true peace is through domination. So, he would begin to gather power, using his skills and charisma, but for the wrong reasons. He would form his own group of followers, who also believe in his new 'world order' ideas, and start a war against the existing shinobi villages.
Well, one possible plot could be Naruto facing various challenges within the village that require the leadership of a Hokage. He might have to deal with political unrest, new threats from outside, and also find ways to improve the lives of the villagers. For example, he could start new training programs for the younger generation to make them stronger shinobi.
The plot could involve Naruto seeing Kakashi as the ultimate ninja and trying to learn all of his non - jutsu related skills. For example, Kakashi is often seen reading his 'Make Out Paradise' books. Naruto might start carrying around a similar - looking book just to be like Kakashi. And in battles, Naruto might use Kakashi - like strategies, such as using misdirection and feints more often.
The plot could involve Naruto being resurrected as a vampire by some dark magic. As a vampire, he is shunned by some in the village at first. But then he discovers that there are other vampires who are planning to take over the ninja world. So he teams up with his old comrades, using his unique combination of ninja skills and vampire abilities to stop them.