It could be about Naruto having a secret power that he discovers late in his journey. Maybe it's a special chakra form that gives him abilities he never thought possible.
Maybe Naruto secretly admires the Uchiha's Sharingan ability and tries to learn more about it on his own. He could be collecting information about the Uchiha clan's history and techniques without anyone knowing.
It could be about Naruto and Hinata going on a secret adventure together. Maybe they discover a hidden place in Konoha that no one else knows about and have to protect it from some sort of threat.
In some naruto secret training fanfiction, the training could be centered around Naruto's connection to the Nine - Tails. He might learn how to tap into the Nine - Tails' chakra in a more controlled and efficient way without the negative side effects. This could involve some spiritual journey within his own mind - scape where he and the Nine - Tails reach a new level of understanding and cooperation, leading to a huge boost in his power.
One possible plot could be that Naruto discovers he has a child during a mission. Maybe he saved a village years ago and unknowingly had a relationship with a local woman. The child could be in danger from some villains who want to use the child's connection to Naruto for their own evil plans.
The plot might involve the child being hidden away for their safety. Since Naruto and Hinata are well - known and powerful, there could be many who would want to harm the child. So they grow up in a secret location, perhaps with only a few trusted people knowing their true identity. As they grow older, they start to discover their heritage and the responsibilities that come with it.
Well, it could be about Naruto and Hinata working on a super - secret ANBU mission together. Maybe they have to infiltrate an enemy stronghold and they discover new things about each other during the mission. Their relationship might deepen as they rely on each other's skills in the dangerous situation.
Well, it could be about Naruto secretly training to become an ANBU member. Maybe he has to hide this from his friends because the ANBU work is so dangerous and secretive.
Maybe Naruto is a secret girl in the sense that he has to disguise as a girl for a mission. And during this time, he discovers a whole new side of the female world in the ninja village. He could learn about the different expectations and challenges that girls face, and this could change his perspective on them.
Well, it could be about Naruto and Hinata's child who turns out to be a secret prodigy. Maybe this child has some unique powers that neither Naruto nor Hinata had expected. For example, the child could have the ability to combine Naruto's Rasengan with Hinata's Gentle Fist in a completely new and powerful way, and the story could revolve around how they discover and train this power.
Perhaps the fanfiction focuses on a secret friendship between Naruto and Ino that they have been hiding from the others. They could be sharing their dreams and fears, and helping each other grow in ways that no one else in the village knows about. For example, Ino might be secretly training Naruto in some mind - related jutsu that she has developed on her own.