Some fanfictions might reveal that Naruto has a secret relationship with a character that was not explored in the main story. For example, he could have a deep connection with a minor character from a different village, which changes the whole perspective of his character in terms of how he interacts with the ninja world.
It could be the secret of Naruto's parentage being more fully explored in a different way than in the original story. Maybe details about his mother's side of the family that were never mentioned before.
It could be an old sage or a hermit who has been watching Naruto from afar. They might decide that the time is right to reveal the secret to Naruto himself or to those around him for the greater good of the ninja world.
Well, it could be that Naruto has a secret about his parents that's darker than we thought. Maybe he found out some negative things about his father's past actions that he's been hiding. For example, perhaps his father had to make some really tough and morally grey decisions during the war that Naruto now has to come to terms with.
In this fanfiction, perhaps Naruto's hidden jutsu legacy could be revealed. Maybe it shows some secret techniques that he developed but never got to show during the original series.
One consequence could be that it changes the way his peers view him. If the fanfiction has some unique or unexpected ideas, it might make them see Naruto in a whole new light. Maybe it could even inspire some of them to start writing their own fanfictions. However, there could also be those who are critical and might tease him about it.
It could also be Kakashi. There might be fanfictions where he has some secrets related to Naruto. For instance, he might be aware of a secret mission related to Naruto that he has been keeping from everyone, which could be a major plot point in the fanfiction.
If Naruto's dark secret is about his family, it could completely change how we view his character arc. It might add a new layer of complexity to his journey of becoming Hokage. For instance, if his father had a dark past, Naruto might have to work harder to prove that he's different and worthy of the title.
One possible secret could be about Naruto's real parents' untold past. Maybe there are hidden details about how his father and mother met that were not in the original story.