Maybe it's an enemy who discovers the secret and uses it to try and undermine Naruto. For example, an enemy might find out about a hidden weakness that is related to the secret and use it to their advantage in a battle. However, this backfires as Naruto overcomes the situation and uses the revelation of the secret to grow stronger. Another possibility is that a close friend of Naruto accidentally stumbles upon the secret. For instance, while exploring an old scroll together, they find something that reveals the long - held secret.
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.
It might also be Anya herself. Since she has telepathic powers, she could accidentally let something slip while reading someone's mind. Or she could be tricked into revealing a secret by someone who realizes she has this special ability. This would create a lot of drama and conflict within the family as they try to deal with the consequences of the secret being out in the open.
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.
Most likely Naruto himself, since it's about his heritage being revealed.
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 secrets about a character's past, like a hidden identity or a past crime they committed.
He might meet the spirit of an ancient ninja who was the keeper of the library. This spirit could guide Naruto through the library and teach him things that no one else in the present day knows.
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.
It could be that a new character, someone from a far - off land that Naruto met during one of his travels, is involved in his secret life. This character could bring with them a different culture and set of skills that Naruto is learning from in secret, perhaps something that could revolutionize the way ninjas in the Hidden Leaf operate.
It could be Gabriel Agreste. He has been a suspect in the original series for various reasons. He is often absent and has a lot of secrets. So in the fanfiction, it would make sense if he was finally revealed as Hawk Moth.