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.
Well, perhaps Naruto was sealed as part of a prophecy. The 1000 - year seal was meant to keep him in stasis until a certain time when the world would be in dire need of his power. While he was sealed, the world faced numerous challenges and wars. Once unsealed, Naruto has to not only regain his strength but also unite the fragmented ninja world which has been divided over the 1000 years.
Maybe it's an ancient evil that was sealed away long before Naruto but managed to break free during his 1000 - year imprisonment. This evil entity now wants to destroy the world and sees Naruto as an obstacle once he is unsealed.
The plot in 'naruto sealed memories fanfiction' could be that Naruto discovers a way to break the seal on his memories accidentally. These memories might contain information about a powerful jutsu or a hidden power within him. As he delves into these memories, he may face challenges like dealing with the emotional impact of what he remembers and also fending off those who would try to stop him from fully exploring and using these new - found memories.
In this fanfiction, a plot twist could be that the seal actually has a secondary effect. Instead of just containing Madara, it also starts to absorb some of his power into Naruto. So Naruto gradually becomes stronger in a very unorthodox way. However, this also comes with risks as the power of Madara might corrupt Naruto's mind. Also, there could be a group of ninjas who believe that Naruto should be killed to ensure Madara is never released. This would put Naruto in a difficult situation where he has to fight not only against the possible corruption within him but also against those who see him as a threat because of Madara's presence inside him.
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.
It could be from an ancient and forgotten clan. Maybe a clan that had the power to tame and seal dragons long ago, and for some reason, they chose Naruto as the vessel for this dragon. Another possibility is that it came from a different dimension where dragons are common, and through some magical accident or ritual, the dragon ended up sealed in Naruto.
He could develop a deeper understanding of chakra control. Being sealed away might have forced him to focus inwardly on his chakra, leading to more refined control. Maybe he can now use chakra in ways he couldn't before, like creating more complex and powerful jutsus with less effort.
Maybe the village has changed a great deal while Naruto was sealed. When he finally breaks free, he has to face a whole new set of challenges and enemies that have emerged in his absence. There could be new political situations in the Hidden Leaf Village as well.
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.
One possibility in fanfiction is that Nagato's sealing is a result of his own guilt. After realizing the extent of the destruction he has caused, he might allow himself to be sealed. This could be a very emotional and character - driven plot point. For example, he may feel that by being sealed, he can atone for his sins. And the story could then explore how the other characters react to this self - imposed seclusion of Nagato, and whether they try to convince him otherwise or accept his decision.