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.
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.
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.
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.
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.
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.
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.
Naruto himself is often very popular in Naruto Secrets Fanfiction. Writers love to explore different aspects of his character, like his hidden potential or his relationships with other characters in new and exciting ways.
He could uncover secrets about his family. There might be some hidden records in the library that reveal things about his father or mother that he never knew before.