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.
Maybe it was an old acquaintance from her academy days. They reconnected later in life, and one thing led to another. But Fem Naruto is worried about how the relationship and the child will be perceived, so she keeps it a secret. This could lead to a story of self - discovery and dealing with past relationships as she tries to protect her child.
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.
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.
Another possibility is Harry Potter himself. This would be a very different take on their relationship. In some fanfiction, the strong bond between Hermione and Harry could be taken to a new level. Maybe in a situation where they are the last hope for the wizarding world, they conceive a child in secret to carry on some special magic or power that could save the wizarding community.
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.
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 Edward. Since they had a deep connection in the original story, it would make sense for him to be the father in the fanfiction.
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.
It could be Ginny. Even though in the original story they are married and have kids in a more normal way, in fanfiction, there could be a twist where their relationship had a secret earlier on and she is the mother of the secret child.
It could be an old acquaintance that Percy had a brief relationship with. Maybe someone he met during one of his adventures and then lost touch with, but she later discovers she's pregnant and decides to keep the child a secret from Percy for various reasons.
The father might be a character who is in a position of power and Sakura is afraid of the consequences if his identity is revealed. For example, he could be a nobleman or a powerful wizard in a magical world. Since having a relationship with him might be frowned upon or dangerous, she keeps the baby a secret.