The story could also focus on the efforts to unseal Naruto. His friends and the characters from the crossover world could embark on a dangerous journey to find the key or the magic to break the seal. In a Naruto - Harry Potter crossover, Hermione might use her vast knowledge of magic to research a way to free Naruto from the seal.
A corrupt leader from a political - based crossover world might be the main antagonist. He views Naruto as a threat to his power, especially with the mystery of his seal. So, he tries to either keep Naruto sealed away permanently or use the situation to gain more control over his own people by creating fear around Naruto's presence in their world.
Another option is that a new character introduced in the crossover could be the main character. For instance, in a Naruto - Fullmetal Alchemist crossover, an alchemist from the FMA world could stumble upon Naruto's sealed state and make it their mission to free him, while also getting involved in the politics and power struggles of the Naruto world.
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.
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.
One idea could be the exploration of how Naruto's sealing affects the crossovers. For example, if it's a crossover with the Bleach universe, the seal might disrupt the spiritual balance there. Another could be Naruto being sealed in a different dimension where the crossover characters reside, and he has to find a way to break the seal while interacting with these new characters.
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 a fanfiction where Naruto sealed away One Piece, it might have a huge impact on the characters. Luffy, for example, would be devastated as his life's goal is to find One Piece. He might even try to find Naruto to convince him to reverse it. The other Straw Hats would also be affected, their dreams of seeing the end of the Grand Line and the secrets One Piece holds vanishing. And the entire pirate community would be shaken to its core, as One Piece is like the ultimate symbol of their freedom and adventure.
One possibility in such a fanfiction scenario is that Kushina's own chakra, which was already special as an Uzumaki, could have an impact on Naruto while he's sealed within her. It could either strengthen him in some ways or cause unforeseen consequences. Also, characters like Minato would have a different relationship with the situation. Instead of seeing Naruto as his son on the outside, he might be more focused on the presence of Naruto within Kushina, which could change how he approaches protecting his family and the village.
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.
In some fanfictions, if Naruto was sealed in the Shinju, it could lead to a major shift in the power balance. His friends might go on a desperate quest to free him. The ninja world could be plunged into chaos as his absence leaves a huge void in terms of power and leadership.