It could be Orochimaru. He has always been interested in power and Naruto's unique abilities. With Naruto sealed away, Orochimaru might see it as a chance to steal whatever power Naruto had or use his absence to further his own evil plans in the ninja world.
One possible plot development could be that the village is thrown into chaos without Naruto. His friends might initially feel lost but then come together to find a way to bring him back. For example, Sasuke could put aside his differences and join forces with the others, realizing Naruto's importance to the village and to him personally.
In such a fanfiction, the Fairy Tail guild might be thrown into chaos. They could initially be confused about this strange event from another world. Some members might see Naruto's sealing as a threat to their world's balance, while others might be more curious and try to find a way to break the seal.
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.
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.
Perhaps Percy discovers a secret that is so dangerous that the powers - that - be decide to seal him away to keep it safe. It could involve a prophecy that he might fulfill in a way that would change the world in a way they don't want. So, they use some ancient magic or a powerful artifact to seal him. For example, if there's a prophecy about Percy uniting two warring factions in a way that would upset the current balance of power, those in power might try to stop it by sealing him away.
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.