Perhaps there was a prophecy that Naruto's godlike powers would attract some great evil. In order to prevent this, the ninja world's leaders chose to seal him away. They might have thought that it was a necessary sacrifice to keep the balance and safety of the world. Also, there could be some dark secrets about his powers that made others believe sealing was the only option.
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.
Well, it changes the power dynamic. With Naruto sealed away, the villages that once relied on his strength would be in a more vulnerable position. His friends and allies would also have to find new ways to protect their homes. It might lead to new alliances forming as different groups try to fill the power vacuum left by Naruto.
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 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.
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.
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.
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.
I'm not entirely sure as I haven't read that specific fanfic. But it might be about Naruto being sealed away in some way, perhaps in a different scenario from the original story. Maybe some new villain or power manages to seal him.
One interesting Naruto fanfiction could be where Naruto is sealed away and his friends have to find a way to break the seal without his power. They might have to seek out ancient knowledge or form unexpected alliances.
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.
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.