Well, perhaps in this fanfiction, the Avatar enters the Naruto universe and causes some sort of imbalance. Naruto, seeing the chaos it might bring, decides to seal away the Avatar. As time passes, Naruto starts to learn more about the Avatar's world and realizes that there are good things about the Avatar too. So he begins a journey to find a way to unseal the Avatar without causing more harm, all while facing enemies who want to use the situation for their own gain.
In this 'Naruto sealed away avatar' fanfiction, it could be that the two worlds of Naruto and Avatar are somehow merging in a bad way. The Avatar's power is too much for the Naruto world to handle at the moment. Naruto, with his knowledge of sealing techniques, seals away the Avatar. But this act has consequences. Naruto has to deal with the political and social unrest in his own world because some people believe he's done something wrong. Meanwhile, he's also trying to figure out how to reverse the seal when the time is right.
It could be Orochimaru. He might have learned about the Avatar's unique power and wants to use it for his own dark experiments. So he tries to break Naruto's seal to get to the Avatar. He would be a great villain as he's always after powerful things and doesn't care about the consequences.
One possibility is that the story could focus on how the village copes without Naruto. Maybe there would be a different kind of unrest or a search for a new way to deal with the Nine - Tails' power. Without Naruto, characters like Iruka might have a different role, perhaps becoming more involved in trying to find a solution to the power void.
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.
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.
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 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.
Maybe Naruto is sealed by a powerful and ancient evil force. During the 1000 years, the world he once knew could change completely. His friends and the Hidden Leaf Village might have long been forgotten or turned into legends. When he is finally unsealed, he has to adapt to this new world and face new threats that emerged during his long absence.
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.
There's also the possibility that it was an accident. Some kind of jutsu gone wrong during the sealing process. The person performing the sealing might have been inexperienced or there could have been some unforeseen interference that led to Naruto being sealed away instead of the Nine - Tails being properly sealed within him.
The main antagonist could be a new character created specifically for the fanfiction. This character might be from a long - lost clan that has a grudge against the Uzumaki clan, of which Naruto is a part. Since Naruto is the last of the Uzumaki in the village, sealing him away would be their first step in getting revenge on the clan, and they would do everything in their power to keep him sealed.