Well, perhaps the story could be about Naruto finding out he has a sister who was hidden away for her own safety. Maybe she has some unique powers that the villains are after, and Naruto has to protect her while also learning about his family's past.
Perhaps the main antagonist is a dark figure from within Konoha itself. This person doesn't want Naruto's family to be reunited because it could expose some dark secrets about their own actions in the past. They would do anything to keep the sister hidden and Naruto in the dark, even if it means causing harm to both of them.
It could be Hinata. In the original series, Hinata has a deep affection for Naruto. In a fanfiction, it would be a natural progression for her to be his secret fiance. Maybe they got engaged secretly to avoid some political unrest in the village.
It might also be Gaara. Their initial encounters were filled with tension, but as the story could be twisted in fanfiction, that could develop into a different kind of relationship. Gaara's own journey of self - discovery and Naruto's influence on him could be a basis for a romantic relationship in fanfic.
Well, it could be a fanfiction where Naruto discovers he has the Mokuton ability in a very unexpected way. Maybe he gets it through some ancient power transfer or a connection to a long - lost clan. And this new power of Mokuton could lead him to face new enemies or form new alliances. It might also explore how his friends react to this new side of him.
It could be that Naruto is secretly training a new and powerful jutsu that he doesn't want anyone to know about yet. Maybe he's afraid that if his enemies find out, they'll try to stop him before he perfects it.
She might feel guilty. Since they are siblings, she could be aware of Naruto's neglect and try to make it up to him in small ways, like sharing her food or secretly leaving him little gifts.
Naruto might team up with Gaara. Gaara has his own unique abilities with sand control. Together, they could form a strong duo for a secret mission, especially if it involves something related to the balance of power between their respective villages.
Well, it could make Naruto extremely powerful right from the start. With the Rinnegan, he might be able to master all types of jutsu more quickly. He could also have an edge in battles against powerful foes like Madara or Kaguya. Maybe he'd be able to use the six paths techniques with more ease and less training.
It could change the relationships Naruto has with other characters. For example, his friends might be shocked at first but then become protective of his daughter. His enemies could see her as a new target or a way to get to Naruto.