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.
One possible secret could be about his training with Jiraiya. Maybe he'll disclose some special techniques that Jiraiya taught him in private that he never showed during the regular battles in the original series. For example, a unique way of using the Rasengan that requires a deeper chakra control.
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.
Another possibility is that he reveals secrets about his parents. He could talk about things his father, Minato, told him in a dream or some information he discovered about his mother, Kushina, that no one else knows. For example, a secret mission they were involved in or a special bond they had with certain characters in the Hidden Leaf Village.
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.
He could uncover the truth about his father's real mission before he died. Maybe it was something that was kept hidden from the village for some reason.
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.
He might uncover a hidden weapon that could change the balance of power in the ninja world.
In the fanfiction, the scrolls could reveal a lot. For example, they might disclose the circumstances of Naruto's birth. Maybe there are prophecies written in them about Naruto's future. There could be stories of his parents' love and how they made sacrifices for the village and for Naruto. It could also be that the scrolls contain some sort of training method that was unique to his family, which would help Naruto become even stronger as a ninja.
One interesting plot idea could be exploring a secret training regime that Naruto discovers. Maybe it was created by an ancient ninja clan and it gives him unique powers. For example, it could involve harnessing the power of natural elements in a different way than normal chakra control.
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.