Another option could be a new character. A mysterious and powerful ninja from another village who Fem Naruto met during a diplomatic mission. They had a short - lived romance, and he doesn't even know about the child. This would add an element of mystery and the potential for the father to show up later in the story.
One possible plot could be that Fem Naruto has been in hiding with her child to protect it from old enemies. Maybe she was in a relationship during a time of peace but things turned bad. Now she's constantly on the move, training her child in secret ninja skills.
Maybe the story focuses on the relationship between Fem Naruto and her child. The child could inherit Naruto's strong will and determination, but also have some traits unique to Fem Naruto. For example, the child might be more empathetic or have a different approach to solving problems. And as the child grows, they start to understand the legacy of their mother and strive to make their own mark in the shinobi world.
It could be a random villager that Naruto met during one of his travels. Maybe she was from a small village that Naruto helped protect, and they had a brief encounter that led to the child.
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.
In this fanfiction, the relationship development could be complex. Naruto, being female in this version, might initially struggle to connect with the demigod child. However, as she discovers more about the child's origin and purpose, she becomes more involved. The story could show them bonding over training sessions where Naruto teaches the child about the ninja world, and the child shows Naruto new ways of using chakra because of its demigod abilities.
In this fanfiction, the demigod child may have the power to communicate with nature spirits. This would give it an edge in understanding the natural world and using it to its advantage. It could also have the power of teleportation, which would be very useful in battles or when they need to escape quickly. Additionally, the child might have enhanced physical strength and speed, making it a formidable force in combat situations.
It could be Sasuke. Their relationship has always been complex in the original Naruto story. In the fanfiction, their relationship might have developed into a romantic one, leading to the birth of the child. The child would then inherit traits from both of them, perhaps Sasuke's cool-headedness and Fem Naruto's determination.
Another possibility is that it's a result of some strange chakra experiment gone wrong (or right). Scientists in the Naruto universe are always dabbling in chakra research. Maybe an experiment meant to enhance her natural abilities instead gives her the Rinnegan, and she then has to learn to control it quickly to avoid being consumed by its power.
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.