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.
Naruto might have developed the ability to sense and manipulate negative emotions. After years of isolation, he could have become attuned to the darker aspects of people's feelings. This could be used in battle to either disrupt his enemies or to help his allies overcome their inner demons. Also, he could have developed a new form of Sage Mode, perhaps one that is more in tune with the spiritual side of nature rather than just the physical elements.
In some fanfictions, Naruto could gain the ability to communicate with spirits or entities that exist in a different plane. Since he was in a state of being sealed, he might have had some kind of connection to the otherworldly. This new ability could give him an edge in gathering information, as these spirits could tell him things about his enemies or about hidden threats to the ninja world. Additionally, his physical strength could have increased exponentially due to the years of being in a state where his body was forced to adapt to the confinement, and now he can use that strength in new and powerful ways.
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.
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.
Another ability Naruto could develop is enhanced stealth. Itachi is known for his stealth and ability to move undetected. During the three - year training, Itachi could teach Naruto how to move more quietly, hide his chakra signature better, and approach opponents without being noticed. This would give Naruto an edge in combat, especially when facing more powerful opponents where a surprise attack could be crucial.
Naruto might be able to create cloud - based illusions. Just as he can create shadow clones, with the power of Cloud sealed in him, he could project illusions made of clouds to deceive his opponents. These illusions could be large - scale and very realistic, confusing enemies about his true location and intentions.
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.
In some Naruto fanfictions, after Hashirama was sealed, it could lead to a power imbalance in the ninja world. His sealing might be a plot device used by the antagonist to gain an upper hand. For example, if a powerful enemy sealed Hashirama away, it would remove one of the most powerful forces that could oppose them, allowing them to carry out their evil plans more freely.
Another possibility is a character who has been corrupted by the same power that was used to seal Naruto. This character could see Naruto's awakening as a threat to their new - found power or status. For example, if the sealing was related to some ancient and dark chakra, a ninja who has been influenced by this chakra might oppose Naruto.
He could develop some sort of psychic power that doesn't rely on chakra. This could be a power related to his willpower, allowing him to influence the minds of his opponents or sense their intentions from a distance.