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 be a way to explore alternative storylines. Maybe in these fanfictions, the author wants to see what would happen if Naruto wasn't there to save the day all the time. So, they make him disappear to introduce new threats and challenges that the female characters have to face on their own, like dealing with a new and powerful enemy.
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.
He could be influenced by a powerful and mysterious force. This force might be something magical or a very strong jutsu that causes him to lose his memory and wander away from his family. In some fanfics, new and made - up powers can often play a role in such situations. Without his memory, he doesn't recognize his family and just drifts away.
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.
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.
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.
One possible reason is that she is in danger. There could be someone or something that wants to harm her or her unborn child, so she has to disappear to stay safe.
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.
It could be that Aang disappears because of a prophecy. He might believe that by disappearing, he can prevent a catastrophic event from happening. His friends, not knowing this, embark on a journey to find him, facing many challenges along the way. They might discover secrets about Aang's past that they never knew before, and these secrets could be the key to bringing him back.
Perhaps Harry is kidnapped by a mysterious and powerful magical being. This being has the ability to make Harry disappear without a trace. His friends then embark on a dangerous quest to find him, facing many magical challenges along the way. They might have to search in hidden and dangerous parts of the wizarding world that they have never been to before.