One possible reason could be for the sake of creating a dramatic plot. The disappearance of Naruto might be used to show how the female characters respond to his absence, highlighting their growth and independence. For example, Sakura might take on more leadership roles in the village without Naruto around.
It could also lead to a loss of trust. If they were using the female henge to gain someone's confidence, like in a diplomatic or social situation within the fanfiction, the sudden disappearance would make others question their motives and integrity.
One possibility could be that Naruto is kidnapped by a hidden enemy right at birth. Maybe a rogue ninja group has a vendetta against the Fourth Hokage and they steal Naruto away. This would lead to a completely different story arc in the Naruto universe, with Konoha perhaps not knowing Naruto's true identity and not treating him as the Jinchuriki. It could also mean that Naruto grows up in a different environment, away from the discrimination he faced in the original story, but also without the friends and support system he eventually had in Konoha.
Orochimaru could be a likely main villain. He has always been interested in Naruto's power and body. Maybe he finally devises a plan to kidnap Naruto and use his body for his own reincarnation experiments.
It could be that Naruto sacrifices himself to seal away a great evil. However, his friends don't believe he's truly gone and embark on a journey filled with self - discovery and growth as they try to find a way to bring him back. Along the way, they might encounter other lost souls or forgotten powers that could potentially help in their quest.
The emotional tone of the story shifts. Naruto is often the source of hope and inspiration in the Naruto universe. His disappearance can create a sense of despair or urgency among the female characters, which drives the plot forward in a different direction. They might have to work harder to keep the morale up in the village.
One possibility is that Naruto is sent on a top - secret mission by ANBU. Maybe he has to infiltrate a powerful enemy organization. His disappearance could be part of a long - term undercover operation where he has to cut off all ties with his friends and the village for a while to avoid suspicion.
One possibility in this fanfiction is that Naruto's training with the Kyuubi helps him to better understand the nature of chakra itself. He could discover new ways to combine his own chakra with that of the Kyuubi, creating a unique and extremely powerful form of energy. This new form of chakra could give him an edge in future battles against powerful enemies. Also, his time training might be filled with various challenges and trials set by the Kyuubi, which would test his resolve and determination, making him an even stronger ninja in the end.
Perhaps he discovers something about his past or his powers that makes him feel he has to leave Konoha to explore it further. For example, he might find out about a hidden place related to the Uzumaki clan and wants to go there alone to uncover the secrets. Or it could be that he has some kind of internal conflict within himself, like feeling unworthy of being in Konoha due to some self - perceived failure, and so he runs away.
The setting in which Harry disappears and returns also matters. If it's in the middle of Hogwarts, the school would be in chaos. Teachers would be trying to keep the students calm while secretly searching for Harry. And when he returns, the reactions of different houses - Gryffindor being relieved and proud, Slytherin perhaps being suspicious - could add more layers to the story.