It might be an ancient and forgotten wizard. In the fanfic world, the author could create a backstory where this wizard had a prophecy about having a daughter who would be very important in the future. So he secretly arranged for Hermione to be born into the wizarding world we know, and he's been watching over her from the shadows all this time.
It could be a powerful wizard who has been in hiding all this time. Maybe someone with a dark past that the author wants to explore.
It could be Ron. Maybe they had a falling out or some complicated situation that led to Hermione keeping the baby a secret from him.
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.
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.
One plot twist could be that her secret father is actually an enemy in disguise. He might have some evil plan that involves Hermione unknowingly.
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.
It could be a mortal man that Artemis fell in love with in secret. Maybe a skilled hunter who caught her eye in the forest one day.
It could be that she is a secret heir to an ancient magical family. In many fanfics, this trope is used to add an extra layer of mystery and power to her character.
It could be Hinata. Even though in the original story they are openly married, in a fanfic scenario, there could be a situation where their relationship was kept secret for some time and she gave birth to a son secretly. Maybe due to some threat to the village or Naruto's safety.
It could be a long - lost relative of Voldemort who has been hiding in the shadows. They might be more cunning than Voldemort and have a different approach to causing trouble in the wizarding world.
Ron could be the father. Given their relationship in the original series, it would be a natural choice. They could have gotten married and had a son. Ron's laid - back nature might contrast with Hermione's more serious side when it comes to parenting their son.