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.
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 way could be through a powerful jutsu. For example, a combined jutsu by his closest friends like Sasuke and Sakura. They could pool their chakra and create a jutsu strong enough to break the seal on the moon. Another option is that there might be some ancient prophecy or knowledge that reveals the key to unsealing Naruto. A hidden ninja clan could possess this knowledge and come forward to help.
His friends would likely be in shock. Sasuke, for example, might initially be angry at himself for not being able to prevent this. He would then start planning ways to break the seal and get Naruto back. Sakura would be heartbroken. She might use her medical skills and knowledge of chakra to try to find a way to communicate with Naruto or at least sense his condition in the moon. Shikamaru, being the strategist, would start gathering information about the seal and who or what caused it.
In many such fanfictions, it could be a variety of deities. It might be an ancient and powerful god from Naruto's world's mythology that the story's author has chosen to insert. For example, it could be a god of elements like a super - powerful fire god, which could give Naruto even more control over his existing fire - based jutsu and new, more extreme abilities related to fire.
In some fanfictions, Kushina was sealed into Naruto through a complex jutsu. It might be a modified version of the sealing jutsu used to seal the Nine - Tails. The process could involve special incantations and chakra manipulations.
In some Naruto fanfictions, Madara might be sealed through a powerful jutsu created by the main character. For example, the protagonist could combine different elemental chakra natures to form a unique sealing technique specifically designed to counter Madara's power.
Well, in some Naruto fanfictions, Bardock might be sealed by powerful jutsu. Maybe a dark ninja uses a forbidden sealing technique to lock him away, preventing him from interfering with their evil plans.
Well, one reason could be that the author wants to explore an alternate universe. Maybe in this fanfiction's version of the Naruto world, the events leading to the sealing of the Kyuubi never occurred. It could be due to different political situations among the ninja villages, or perhaps a different chain of events that prevented the Kyuubi's attack on Konoha in the first place. So, without the attack, there was no need for the seal.
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.