It could be Naruto himself. As he grows and faces new challenges, he might stumble upon these secrets, either by accident or through his own determination to learn more about his world and his place in it.
Sasuke could be one of the characters aware of Naruto's secrets. Given their intense rivalry and deep friendship, Sasuke might have noticed something odd about Naruto and dug deeper to find out. Maybe Naruto let something slip during one of their battles or emotional conversations.
One possible secret could be that Naruto has a hidden power passed down from an ancient clan that he discovers later in the fanfiction. Maybe it's a special chakra ability that gives him an edge in battles.
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.
In this fanfiction, Naruto might reveal his insecurities about being the Jinchuriki at first. He could share how he was really scared of the Nine - Tails inside him and how he had to constantly battle with the fear of losing control.
Another idea is that Naruto has a dark secret regarding his past training. Maybe he had to do some unethical or dangerous things during his training with Jiraiya that he's ashamed of. This could include using forbidden jutsu or making deals with dark entities in order to gain power, which would be a huge shock to his friends and the village if it ever came out.
Kakashi could be involved too. Given that Kakashi has trained Naruto and seen his growth, Naruto might trust him with his secrets. He could reveal his thoughts on how he wants to change the ninja world for the better and the steps he is planning to take in the future.
Well, it could be a unique kekkei genkai that has been given an ultimate defensive quality in the fanfiction. For example, a power that allows the user to transform into an indestructible form, similar to how Gaara can use his sand as a shield but much more powerful. This form could be able to deflect all kinds of attacks, whether they are physical, ninjutsu - based, or genjutsu - based.
Yes, he can be. Fanfiction is a realm of boundless creativity. If an author wants to reimagine Naruto as an ultimate demon, they can. Maybe they rewrite his backstory to include some dark and demonic elements. For example, his connection to the Nine - Tails could be made more sinister, and his powers could be redefined to be more demonic in nature, like having the ability to spread chaos and destruction.
The dark secrets can add a lot of tension to the plot. If Naruto has a secret related to an evil organization, it could make his friends and allies question their trust in him. They might start to suspect his every move, and Naruto would have to struggle to prove his loyalty while also dealing with the truth of his situation.