The main character is Naruto. But other characters like Jiraiya could be very important. Jiraiya was aware of Naruto's heritage to some extent and could be the one to fully disclose it to Naruto in the fanfic. Also, characters from the Uzumaki clan, if they are still alive in the fanfic's universe, could be main characters. They could help Naruto embrace his heritage and teach him about the clan's traditions.
Well, in many such fanfics, a key plot point could be Naruto finally learning about his Uzumaki heritage which gives him access to unique powers and abilities. Maybe he discovers secrets about his family's past that were hidden from him. Another point could be how he uses this newfound knowledge to gain respect in the village, as the Uzumaki clan was once highly respected.
Well, it could strengthen his bonds. His friends might see him in a new light, with more understanding and respect. For example, they could realize the weight of his past and be more empathetic towards his struggles.
It's possible he gains enhanced physical abilities like super strength or speed. Since his heritage is often tied to some special genetic traits, these could be unlocked upon the revelation. For example, if his heritage is linked to a powerful clan, he could inherit their natural combat prowess. He could also find out about special chakra control abilities that are exclusive to his bloodline, which would give him an edge in battles.
He might feel angry and frustrated. Naruto has always been proud of his potential and his roots in some way. Being denied his heritage would be like taking away a part of his identity, so he'd likely be quite mad at those who are doing the denying.
One consequence could be a loss of self - confidence. His heritage has been a part of what has motivated him to become stronger. Without that connection, he may start to doubt his abilities.
One possible reason could be the burden that comes with his heritage. Naruto's heritage is filled with great power and responsibility. Maybe he feels that he can't live up to the expectations of his clan or predecessors, so he rejects it.
Maybe he's been influenced by someone who has a different view of heritage. For example, if he meets a character who believes that one should create their own identity rather than relying on heritage, Naruto could be swayed. Another possibility is that he has some sort of resentment towards his heritage. Perhaps there are things in his family's past or in the traditions associated with his heritage that he doesn't agree with or is ashamed of.
Obviously, Naruto himself is a key character as the story is about him learning his heritage. His mentor, like Kakashi, could also play an important role. Kakashi might notice some strange things about Naruto's abilities and start to suspect that there's more to his heritage. Then he could guide Naruto in the discovery process.
In the fanfic, Naruto may learn of his heritage through a new character. Maybe a mysterious ninja shows up who has some connection to his family. This ninja could start to train Naruto in ways that are specific to his family's ninja techniques, revealing more about his heritage as they train together.