Maybe the Rinnegan is not just a normal Rinnegan. It could be a mutated form that has powers beyond what anyone expected. As the story progresses, the protagonist discovers these new powers bit by bit, which completely changes the power dynamics in the Naruto world and makes everyone who neglected him scramble to get on his side.
A really interesting plot twist could be that the neglect was all part of a grand plan by a powerful, hidden enemy. This enemy wanted the Rinnegan user to be isolated so that they could manipulate him more easily. However, the protagonist figures out the plan and instead uses the situation to his advantage. He pretends to be under the enemy's control while actually gathering information and allies to take down the real enemy, thus turning the tables on those who neglected him.
One possible plot could be that the main character, who has the Rinnegan but has been neglected in the original Naruto story, decides to form their own ninja clan. They use their Rinnegan powers in unique ways to train their clan members and rise to power. This would be a new take on the Naruto universe and could explore the untapped potential of the Rinnegan.
Well, perhaps the protagonist uses the powers of the Rinnegan in secret. He might train alone and develop unique abilities that others are unaware of, so that when the time is right, he can surprise everyone who has neglected him.
Well, perhaps in the fanfiction, the neglected Rinnegan was actually a key to an ancient prophecy. Naruto, being the protagonist, starts to notice strange things related to the Rinnegan. He could then embark on a journey to understand its true significance. Along the way, he might meet old enemies who now have a newfound interest in the Rinnegan because of its newly discovered potential.
A really cool plot twist could be that the Rinnegan in Naruto is not a normal one. It has a hidden power that was sealed away by the Sage of Six Paths long ago. As Naruto unlocks this power, he realizes it's linked to a prophecy that he initially didn't understand, and it changes his whole perception of his role in the ninja world. This would involve a lot of self - discovery and new challenges for Naruto.
Well, it might be about Naruto being bestowed with the Rinnegan in a way that's connected to a dark deity. The story could then explore how Naruto has to adapt to this new power. He might struggle with the darker impulses that come with the godlike Rinnegan. For example, the power could make him more ruthless in battle, and he has to find a balance between using this new strength and maintaining his moral code. It could also lead to new alliances and enemies, as different factions in the ninja world react to his transformation.
One plot twist could be that the curse mark is actually a key to unlocking an ancient and powerful jutsu that only fem Naruto can perform. This would change the whole dynamic of the story as she has to figure out how to use it without being consumed by the mark.
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.
A possible plot twist is that the dark godlike Naruto is actually a key to saving two colliding universes. He has to use his powers in a way that no one expects, like sacrificing his own powers to create a new balance. In the crossover aspect, if it's with a post - apocalyptic world, Naruto's positive attitude could be a shock to the survivors there. They might initially be suspicious of him but then realize he can help them. Also, Naruto could find out that his dark powers are linked to a prophecy in the crossover world that predicts either destruction or salvation depending on how he uses them.
Perhaps a plot twist could be that Naruto and Madara's mother was from a powerful and secret clan. This clan has a prophecy about two brothers saving or destroying the shinobi world. Naruto and Madara are unaware of this prophecy until later in the story. As they start to discover their true potential together, they realize that they have a choice to make. This could lead to internal struggles within each of them as they decide whether to fulfill the 'saving' part of the prophecy or be swayed by Madara's past desires for power and destruction. It would add a layer of mystery and moral dilemma to the fanfiction.
One possible plot twist could be that Naruto's awakening of the Rinnegan is not a natural occurrence. Maybe it's the result of a long - hidden jutsu or a curse placed on him by an ancient enemy. This could lead to Naruto having to struggle not only with the new power but also with the implications of how he got it.