A plot for this type of fanfic could revolve around Naruto's inner turmoil. He could be constantly haunted by the question of why his parents neglected him. This could lead him to make some bad decisions, like getting involved with the wrong people. However, through a series of events, he starts to realize that he can create his own family and support system. He then begins to build a new life for himself, one that is not defined by his parents' neglect but by his own strength and the relationships he chooses to cultivate.
A possible plot is that Naruto is constantly bullied because of his neglected state and his unknown bloodline. As he grows, he starts to show signs of his bloodline powers, which attracts the attention of both friends and foes. His journey then becomes about controlling his powers and dealing with the past neglect of his parents while also facing the new challenges that come with his revealed bloodline.
One plot twist could be that Naruto discovers his parents had a very good reason for their neglect, like they were protecting him from a greater danger. Another could be that the village elders knew about the neglect but did nothing, and Naruto has to confront them. Or perhaps Naruto finds out he has a secret power that was the cause of his parents' seeming neglect, as they were afraid of what he could do.
Well, this fanfic might start with Naruto's early days in the village where he's constantly ignored or even shunned. As he grows, he could start to develop his own power in secret, away from the prying eyes of those who neglected him. It could also delve into his relationships, like how his friendship with Sasuke might be affected by his feelings of neglect. And perhaps he'll find a way to prove himself not just to the village, but also to himself, in a much more complex and darker path compared to the original Naruto story.
One common plot point is Naruto's search for his identity. Since he's neglected by his parents, he has to figure out who he is on his own. And with the Mokuton aspect, it often involves uncovering a hidden family connection related to Mokuton. Another is his struggle to gain power. He's determined to become strong using Mokuton to prove that he can succeed without his parents' support.
The plot might involve Naruto being shunned by the Gremory family or their associates. This could lead to Naruto having to find his own path. He could encounter other outcasts or those who also feel neglected. Together, they might form an alliance to change the perception of the Gremory family towards them or to simply make a place for themselves in this world that seems to not want them.
One possible plot could be that Naruto is left alone in his small apartment most of the time as a baby. He might cry for long periods without anyone coming to comfort him. Maybe the villagers, still bitter about the Nine - Tails, avoid helping him. As a result, Naruto grows up with a deep sense of loneliness and a longing for attention from an early age.
In fanfiction, Naruto having the Rinnegan and being neglected by parents can lead to some really interesting character development. It could make him more self - reliant and distrustful at first. He might have to learn to harness the power of the Rinnegan on his own, without any parental guidance. This could result in him making some mistakes along the way but also growing stronger in unique ways.
In this type of fanfiction, Naruto could have a different attitude towards authority. As his parents are neglecting him, he might not have that natural respect for figures of power. He may question the village's system more. Also, his dreams of becoming Hokage could take on a new meaning. Instead of just seeking recognition, it could be a way for him to create a family - a village where no one is neglected like he was by his parents.
In a 'neglected Naruto runs to Uzu' fanfic, perhaps Naruto, feeling unwanted in Konoha, decides to seek out Uzushiogakure (Uzu). He might hope to find a place where he is accepted. Along the way, he could face various challenges like natural obstacles and maybe run into some bandits. He might also start to discover hidden powers within himself during this journey as he is forced to rely on his own strength.
Well, perhaps Naruto, feeling neglected in his own village, decides to seek a new start in Kiri. He might meet new friends and allies there, like some of the unique ninja in Kiri. He could also face challenges from those who are suspicious of an outsider joining their ranks.