It could also be due to some unforeseen consequences of a powerful jutsu. For example, Naruto might have been trying to perform a jutsu to protect the world from a greater danger, but something went wrong. The jutsu backfired and instead of achieving its original purpose, it sent Naruto to be sealed in the moon. The jutsu might have interacted with some sort of lunar energy or ancient seal on the moon that caused this unexpected result.
One possible reason could be a powerful enemy's plot. Maybe an ancient or new villain with great power managed to capture Naruto and used some sort of dark magic or jutsu to seal him in the moon. This villain might see Naruto as a huge threat to their plans and sealing him in the moon is a way to keep him out of the way.
One possible reason could be a misjudgment by the Hokage. Maybe they believe Naruto's power is too dangerous and uncontrollable at a certain point, so they decide to seal him away to protect the village. For example, if Naruto's Nine - Tails' power starts to go berserk and they see no other way to stop it without harming him too much.
In certain fanfictions, Kushina being sealed in Naruto could be related to a prophecy. It might be seen as a way to ensure Naruto's growth and development into a powerful shinobi. The sealing could be a means of giving him an edge, like an extra boost of chakra or some special abilities that are unique to Kushina. It could also be a way to connect Naruto more deeply with his Uzumaki heritage.
A storyline could be that the seal holding Kushina inside Naruto starts to weaken for some reason. As a result, Naruto has to deal with the emerging consciousness of Kushina while also trying to keep it a secret from his friends. This internal struggle could lead to some interesting character development and new plot twists.
One possible reason could be that his godlike powers were seen as a threat. The village elders or some powerful forces might have feared that Naruto, with his immense strength, could lose control and cause destruction. So, they decided to seal him away to protect the village and the world at large.
In such a fanfiction scenario, many things could occur. One possibility is that the world would be thrown into chaos as Naruto is a major force for stability. His friends might embark on a dangerous mission to rescue him. They would have to figure out the mechanism of the seal on the moon and find a way to break it. It could also lead to power struggles on Earth as various factions try to take advantage of Naruto's absence.
It could also be a part of his training or self - discovery. Naruto might have realized that he was relying too much on his chakra and wanted to find a new way to be strong. By sealing off his chakra, he could focus on other aspects like his physical strength, strategic thinking, or even his ninja skills without the use of chakra.
In some fanfictions, it could be due to a miscalculation during a powerful jutsu battle. For example, if they were trying to seal away an even greater threat together, but something went wrong and they ended up being sealed instead. This could lead to a whole new set of adventures for the other characters in the Naruto world as they try to figure out how to free them.
In a fanfiction where Naruto is sealed away, there could be a focus on the emotional turmoil of his friends and family. Hinata, for example, might be extremely distraught and use her Byakugan in new ways to try and find Naruto. Sasuke could also return to the Leaf Village out of loyalty to Naruto and join the efforts to unseal him. The story could also explore how the younger generation of ninjas, inspired by Naruto's legacy, strive to become stronger to free him.
One possible consequence is that the power balance in the ninja world is completely disrupted. With the Kyuubi's massive chakra and power running free, smaller villages might be constantly in fear of being attacked. Konoha, in particular, would have to find new ways to defend itself without relying on the fact that the Kyuubi is sealed within one of its shinobi.
Well, perhaps the writer wants to break the mold of the traditional Naruto story. In the original, Minato is a great father figure, but in this fanfiction concept, the writer might be aiming to show how an alternate reality could shape Naruto. Maybe they want to explore themes of trauma and how Naruto could overcome it. Or it could be a way to experiment with different character dynamics, seeing how Naruto would interact with a Minato who is not the loving father we expect. It could also be a form of creative exploration of the characters' personalities, pushing the boundaries of what we think we know about them.