Perhaps in this fanfiction, new villains emerge seeing Naruto's absence as an opportunity. They could start causing havoc, forcing the remaining shinobi to dig deep into their abilities and form new alliances. This could lead to the discovery of hidden powers among characters who were previously in Naruto's shadow.
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 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.
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.
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 fanfictions of this kind, the wolf sealed in Naruto might have a past connection to a long - lost clan or an ancient evil. This could lead to Naruto uncovering secrets about the ninja world that were previously unknown. Maybe the wolf was sealed for a reason related to protecting a powerful artifact or prophecy, and Naruto now has to deal with the consequences of that.
In this fanfiction, perhaps Naruto uses the Caged Bird Seal to his advantage in a unique way. For example, he could find a way to tap into the seal's energy and use it in his battles. This could make his fight scenes more intense and unpredictable. Also, the seal might attract the attention of some powerful enemies or allies who are interested in its power.
In some of these fanfictions, Naruto goes back and tries to save his parents. He might use his knowledge of the future to outwit the enemies that were once too powerful for his family. Also, he could introduce new jutsus earlier in the timeline, which would change the power dynamics in the ninja world. And sometimes, he gets involved in the politics of the village much earlier, trying to make Konoha a more just place from the start.
Perhaps Naruto's relationship with the other villagers changes more rapidly. In the original story, they were initially afraid of him because of Kurama. But with all of Kurama sealed in him from the start, they might be more in awe or more fearful, which could lead to different interactions. He might also have a different standing among the ninja in his village, being seen as a more immediate and powerful asset or threat, depending on how they view the power of Kurama.
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 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.