It could be a member of an ancient clan thought to be extinct. This would give him access to unique powers and knowledge that no one else in the village has. For instance, if he was secretly part of a clan that could control the elements in a completely different way than normal shinobi.
In some fanfictions, Hinata could be considered as Naruto's secret lover. Since she has a long - standing admiration for Naruto in the original series, it's not a stretch for fanfiction writers to explore a more secretive or different kind of relationship between them.
There are also some fanfictions where a completely new character is introduced as Naruto's secret girlfriend. This allows the writer to create a unique story line and explore different dynamics that are not bound by the pre - existing characters and relationships in the Naruto universe.
In Naruto fanfiction, the jutsus often play a crucial role. When combined with a 'league' - like a group of ninjas - and secret identities, it can create really exciting plots. For example, a ninja could have a secret jutsu that he uses only when his secret identity within the league is at stake. This adds mystery and suspense to the story.
It could be about Naruto having a hidden power that no one in the original story knows. Maybe a power that was passed down secretly in his family.
It could be Kakashi. Since Kakashi has a wealth of knowledge and experience, he might take Naruto on a secret training journey. He could teach Naruto some advanced sharingan - related techniques that Naruto can adapt to his own fighting style, even though he doesn't have the sharingan himself.
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.
It could be that she is a secret heir to an ancient magical family. In many fanfics, this trope is used to add an extra layer of mystery and power to her character.
Naruto himself could be one of the main characters. Imagine if he discovers a secret tattoo on his body that he didn't know about before. It could lead him on a whole new adventure to figure out what it means and where it came from.
There could be some traditionalist ninja in the village who oppose Naruto because she's a girl trying to break the norms. They might see her as a threat to the traditional male - dominated ninja culture and try to stop her from achieving her dreams and rising in the ranks of the ninja world.