In such a fanfiction, Naruto might disappear due to some time - space ninjutsu gone wrong at his birth. He could end up in a different dimension or era. For example, he might be sent to a time when the ninja world was just beginning to form. This would give him a chance to learn different types of ninjutsu and knowledge that was lost over time. He could return to his own time later as a much more powerful and different ninja, changing the power dynamics in the Hidden Leaf Village.
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.
Perhaps at birth, Naruto is taken by a secret organization that wants to use his potential as the Jinchuriki for their own evil purposes. They raise him in isolation and train him to be their weapon. However, as Naruto grows, he starts to question their motives. This could lead to an internal struggle within Naruto as he tries to break free from their control and find his true identity and place in the world.
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.
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.
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.
One possible plot could be that a powerful and secret organization kidnaps Naruto at birth to use his special chakra for their own dark purposes. They keep him hidden away, training him to be a weapon against the Hidden Leaf Village. However, as Naruto grows, he starts to question his captors' motives and tries to break free to find out about his true heritage.
One possible plot could be that Naruto is found by a group of outcasts. They decide to raise him away from the Hidden Leaf Village. As he grows, he discovers his own unique powers that are different from the normal ninja skills in the village. He then has to decide whether to return to the village that abandoned him or create his own path with his new family.
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 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.
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.
Perhaps the fanfiction focuses on how the baby changes the relationships in Naruto's life. Her relationship with Sasuke could be affected, whether they are friends or something more. The baby could also bring new unity among the ninja villages as everyone comes together to protect the new life. And the story could explore how female Naruto passes on her ninja values to her child from a very young age.
The plot could revolve around the build - up to the birth. There might be some pre - birth challenges like Sakura having to take a break from her ninja duties and Naruto having to take on more responsibilities in the village. Then comes the day of birth. Sakura goes into labor and the whole village is on edge. Naruto is right by her side, and they both experience the joys and pains of bringing a new life into the world.